Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_012501875.1 CPAR_RS03180 homoserine O-acetyltransferase
Query= SwissProt::A9I0E6 (424 letters) >NCBI__GCF_000020505.1:WP_012501875.1 Length = 356 Score = 231 bits (588), Expect = 3e-65 Identities = 139/343 (40%), Positives = 189/343 (55%), Gaps = 27/343 (7%) Query: 39 PLPLASGQSLQSYELAVETYGTLNAGRTNAVLVCHALNASHHVAGLAADDPNDVGWWDNM 98 P PL G L ++A T+GTLNA ++N +LVCHAL + AD + WW M Sbjct: 22 PFPLELGGELPELKIAYRTWGTLNAQKSNVILVCHALTGN-------ADADS---WWRGM 71 Query: 99 VGPGKPLDTNRFFVIGVNNLGSCFGSTGPASINPATGHPWGAAFPVLTVEDWVHAQARLA 158 G GK D + F+I N +GSC+GSTGP S+NP +G +G FP +T+ D V AQ L Sbjct: 72 FGEGKAFDETKDFIICSNVIGSCYGSTGPLSLNPKSGKRYGPDFPRITIRDMVAAQRLLL 131 Query: 159 DHFGIERFAAVMGGSLGGMQALSWAITCPERVAHCIVIASTPRLSAQNIGFNEVARRAII 218 FGIE+ V+G SLGGMQ L W PE + + + R SA I +E R+AI Sbjct: 132 QSFGIEKIKLVIGASLGGMQVLEWGAMYPEMAGALMPMGISGRHSAWCIAQSEAQRQAIA 191 Query: 219 TDPDFHGGDYYAHNTVPRRGLSVARMIGHITYLSDDDMAEKFGRTQREPAEGGAYRYGYD 278 D ++ GG +Y PR+GL+ ARM+ TY ++ E+FGR QRE D Sbjct: 192 ADAEWQGG-WYDPAQQPRKGLAAARMMAMCTYRCFENYEERFGREQRE-----------D 239 Query: 279 VEFEVESYLRYQGEKFSRYFDANTYLLITRALDYFDPARGTGGDLARALKPAQADFLLVS 338 FE ESY+R+QG+K FDANTY+ +TRA+D D RG A AL ++S Sbjct: 240 GLFEAESYMRHQGDKLVGRFDANTYITLTRAMDMHDLGRGRESYEA-ALGAFTMPVEILS 298 Query: 339 FSTDWRFPPERSREIVRALLKNGSPVTYAEIDAPHGHDAFLLD 381 +D +P + E+ R L GS + + +D P+GHDAFL+D Sbjct: 299 IDSDILYPKQEQEELAR--LIPGSRLLF--LDEPYGHDAFLID 337 Lambda K H 0.320 0.137 0.427 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: 376 Number of extensions: 24 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: 424 Length of database: 356 Length adjustment: 30 Effective length of query: 394 Effective length of database: 326 Effective search space: 128444 Effective search space used: 128444 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