Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_012474259.1 CPHAMN1_RS04120 homoserine O-acetyltransferase
Query= SwissProt::A0A0I9QGZ7 (379 letters) >NCBI__GCF_000020545.1:WP_012474259.1 Length = 357 Score = 246 bits (628), Expect = 7e-70 Identities = 140/351 (39%), Positives = 203/351 (57%), Gaps = 23/351 (6%) Query: 23 LENGKTLPRFDLMIETYGELNAEKNNAVLICHALSGNHHVAGKHSAEDKYTGWWDNMVGP 82 LE G LP + T+G L+ E+NN +L+CHAL+G A D WWD M G Sbjct: 22 LELGGELPEVSVAYRTWGSLSRERNNVILVCHALTG---------AADADV-WWDGMFGE 71 Query: 83 GKPIDTERFFVVGLNNLGGCDGSSGPLSINPETGREYGADFPMVTVKDWVKSQAALADYL 142 G+ D + F++ N LG C G++GPLS NP +G+ YG +FP VT++D VK Q L D L Sbjct: 72 GRGFDPAKDFIICSNVLGSCYGTTGPLSRNPHSGKPYGPEFPAVTIRDMVKLQRLLLDEL 131 Query: 143 GIEQWAAVVGGSLGGMQALQWAISYPERVRHALVIASAPKLSTQNIAFNDVARQAILTDP 202 GIE+ VVG SLGGMQAL+W +P+RVR + + + + S IA ++ RQAI D Sbjct: 132 GIEEIKLVVGASLGGMQALEWGCMFPDRVRAIMPMGVSGRHSAWCIAQSEAQRQAIAADR 191 Query: 203 DFNEGHYRSHNTVPARGLRIARMMGHITYLAEDGLGKKFGRDLRSNGYQYGYSVEFEVES 262 D+N+G Y N PARGL ARMM TY + + +FGR+ R V F+ ES Sbjct: 192 DWNDGWYEPGNP-PARGLAAARMMAMCTYRSFENFQIRFGREKRD-------EVTFQAES 243 Query: 263 YLRYQGDKFVGRFDANTYLLMTKALDYFDPAADFGNSLTRAVQDVQAKFFVASFSTDWRF 322 YLR+QG+K V RFDANTY+++T+A+D D + G R ++ + + S ++D + Sbjct: 244 YLRHQGEKLVSRFDANTYIVLTRAMDTHDLSRGRG-EYARVLESLTMPVAILSITSDILY 302 Query: 323 APERSHELVKALIAAQKSVQYIEVKSAHGHDAFLMEDEAYMRAVTAYMNNV 373 E ELV+ + A +++Y+ ++GHDAFL+E + R V + + + Sbjct: 303 PQEEQEELVRHIPHA--TIEYLH--ESYGHDAFLIEVDKVSRLVKTFRDEI 349 Lambda K H 0.319 0.135 0.408 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: 360 Number of extensions: 18 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: 379 Length of database: 357 Length adjustment: 30 Effective length of query: 349 Effective length of database: 327 Effective search space: 114123 Effective search space used: 114123 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