Align Homoserine O-succinyltransferase; HST; EC 2.3.1.46; Homoserine transsuccinylase; HTS (uncharacterized)
to candidate WP_011307393.1 MBAR_RS12890 homoserine O-acetyltransferase
Query= curated2:A0LCI7 (394 letters) >NCBI__GCF_000195895.1:WP_011307393.1 Length = 579 Score = 263 bits (672), Expect = 1e-74 Identities = 125/252 (49%), Positives = 171/252 (67%), Gaps = 11/252 (4%) Query: 9 SVGIVTPQHVRLFGASTPLQLDGGTLLHSVDVSYETYGTLNQERSNAVLICHALSGNAHA 68 ++G+V + + G +L+ G L V + YE YG +N ++SN +L+CHAL+G+AHA Sbjct: 21 NLGLVRSMNYEIPGI---FRLESGKTLSHVRIEYEMYGKMNADKSNVILVCHALTGDAHA 77 Query: 69 AGYHSKDDKRPGWWDHYIGPGKPFDTNRYFVIASNNLGGCDGTTGPSSIDPATGMPYGLN 128 AG+H+ DK+PGWW+ IGP K FDT RY ++ SN +GGC G+TGPSSI+P TG PYG++ Sbjct: 78 AGFHT-GDKKPGWWNIVIGPNKAFDTERYCIVCSNIIGGCKGSTGPSSINPETGKPYGIS 136 Query: 129 FPMITIGDIVRVQHALVRQLGIERLMAVVGGSMGGMQALQWALDYPHMVPASVIIAAAPR 188 FP++TI D+V Q LV LG+++L AV GGSMGGMQ LQW + YP MV ++ IA Sbjct: 137 FPILTIADMVNAQKKLVEHLGVKQLFAVAGGSMGGMQVLQWTVSYPEMVKKAIAIATTAS 196 Query: 189 LTAQNIAFNAVARQAIMADPHFNGGDYYTLPGDPTTKARPESGLALARMMAHITYLSEQG 248 T Q IAF A+ R+AI DP +NGG+YY K P GLALARM+ HITYLS+ Sbjct: 197 TTPQQIAFGAIGRKAITDDPKWNGGNYY-------GKKTPAQGLALARMIGHITYLSDAS 249 Query: 249 LHERFGRRLQDR 260 + ++FGR Q++ Sbjct: 250 MQKKFGRDKQEK 261 Score = 93.6 bits (231), Expect = 1e-23 Identities = 49/112 (43%), Positives = 71/112 (63%), Gaps = 1/112 (0%) Query: 271 FAVESYLSYQGSSFVKRFDANSYLYITKAMDYFDPFPDAETTVQRLTGVESHFLVMSFDT 330 F VESYL++QG +F KRFDANSYLYITKA+D+FD + + ++ L+ V + +LV+S + Sbjct: 345 FQVESYLNHQGDTFTKRFDANSYLYITKAVDFFDLSKNG-SLIEGLSVVTAKYLVISITS 403 Query: 331 DWRFDTSRSKELVRILHRSLKDCTFQEFSSPAGHDAFLLPHPSYEKSLGSFL 382 DW + +S+E+V L + D ++E S GHDAFLL + FL Sbjct: 404 DWLYPPYQSQEIVSALTANGVDAKYEEIRSQYGHDAFLLEEGQLNYLIRGFL 455 Lambda K H 0.320 0.136 0.417 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: 548 Number of extensions: 23 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 394 Length of database: 579 Length adjustment: 33 Effective length of query: 361 Effective length of database: 546 Effective search space: 197106 Effective search space used: 197106 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: 51 (24.3 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