Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_011813748.1 HHAL_RS04840 homoserine O-acetyltransferase
Query= SwissProt::Q88CT3 (379 letters) >NCBI__GCF_000015585.1:WP_011813748.1 Length = 382 Score = 542 bits (1396), Expect = e-159 Identities = 249/373 (66%), Positives = 301/373 (80%), Gaps = 1/373 (0%) Query: 6 PEDSVGLVVPQTARFDEPLALACGRSLASYELVYETYGTLNASASNAVLICHALSGHHHA 65 P DSVGLV A F+EPL L CGR L YELVYETYG LN +NA+L+CHALSG+HHA Sbjct: 6 PTDSVGLVTQHKATFEEPLPLVCGRELPRYELVYETYGELNREGTNAILVCHALSGNHHA 65 Query: 66 AGYHAATDRKPGWWDSCIGPGKPIDTNRFFVVSLNNLGGCNGSTGPSSVNPATGKPYGAD 125 AGYH+ DRKPGWW++CIGPGKP+DTNRFFVV NNLGGC+GSTGP+S+NP TGKPYG Sbjct: 66 AGYHSEHDRKPGWWETCIGPGKPLDTNRFFVVCSNNLGGCHGSTGPASINPETGKPYGDQ 125 Query: 126 FPVLTVEDWVHSQVRLGERLGIQQWAAVVGGSLGGMQALQWTISYPERVRHCVDIASAPK 185 FP++TV DWV SQ RL + LGI+QWAAV GGSLGGMQA+QW I YPER+RH + IA+AP+ Sbjct: 126 FPIVTVRDWVRSQARLADELGIRQWAAVAGGSLGGMQAMQWAIDYPERLRHAIVIAAAPR 185 Query: 186 LSAQNIAFNEVARQAILTDPEFHGGSFQDQGVIPKRGLMLARMVGHITYLSDDSMGEKFG 245 LSAQNI FNEVARQAI++DPEFHGG + D GV P+RGL +ARM+GHITYLSDD+M KFG Sbjct: 186 LSAQNIGFNEVARQAIMSDPEFHGGRYYDYGVSPRRGLAVARMLGHITYLSDDAMRAKFG 245 Query: 246 RELKSDKLNYDFHSVEFQVESYLRYQGEEFSGRFDANTYLLMTKALDYFDPAATHGGDLA 305 R+L+ D +++DF V+F+VESYLRYQG+ F FDANTYLLMTKALDYFDPAA H D + Sbjct: 246 RDLRGD-MSFDFEQVDFEVESYLRYQGQRFVQDFDANTYLLMTKALDYFDPAADHDDDFS 304 Query: 306 ATLAHVTADYCIMSFTTDWRFSPARSREIVDALMAARKNVCYLEIDSPYGHDAFLIPTPR 365 A LAH+ ++SF++DWRF+PARSREI+ AL+ K V Y+EI++ GHDAFL+P R Sbjct: 305 AALAHIQCSTLLLSFSSDWRFAPARSREILRALLEHNKPVSYMEIEATQGHDAFLMPIQR 364 Query: 366 YMQGFSNYMNRIA 378 Y++ FS YM +A Sbjct: 365 YLEAFSAYMGNVA 377 Lambda K H 0.320 0.136 0.421 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: 504 Number of extensions: 19 Number of successful extensions: 2 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: 379 Length of database: 382 Length adjustment: 30 Effective length of query: 349 Effective length of database: 352 Effective search space: 122848 Effective search space used: 122848 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