Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_038202407.1 Q392_RS05130 homoserine O-acetyltransferase
Query= SwissProt::Q2T284 (381 letters) >NCBI__GCF_000745855.1:WP_038202407.1 Length = 374 Score = 553 bits (1426), Expect = e-162 Identities = 272/373 (72%), Positives = 309/373 (82%), Gaps = 4/373 (1%) Query: 7 VAPHTMHFAEPLRLQSGSVLGNYQLVVETYGELNAARSNAVLVCHALNASHHVAGVYADD 66 V P +M FA PL L+SG+ LG+Y L ETYG LNA RSNAVLVCHALNASHHVAG YA Sbjct: 5 VTPQSMSFAAPLALRSGASLGDYTLAYETYGTLNAERSNAVLVCHALNASHHVAGRYAGQ 64 Query: 67 PRSTGWWDNMVGPGKPLDTNRFFVIGVNNLGSCFGSTGPMSIDPATGTPYGARFPVVTVE 126 P+S GWWDNM+GPGK +DT+RFFVIG+NNLGSCFGSTGPM ++PATG YGA FPVVTVE Sbjct: 65 PKSEGWWDNMIGPGKAVDTDRFFVIGINNLGSCFGSTGPMHVNPATGRVYGADFPVVTVE 124 Query: 127 DWVHAQARVADAFGIERFAAVMGGSLGGMQALAWSLLYPERVAHCIDIASTPKLSAQNIA 186 DWV AQAR+ DA GI+ AAVMGGSLGGMQAL+W+L YPERV H IAS P L+A+NIA Sbjct: 125 DWVDAQARLLDALGIDTLAAVMGGSLGGMQALSWTLQYPERVRHAAVIASAPNLNAENIA 184 Query: 187 FNEVARSAILSDPDFHGGDYYAHGVKPRRGLRVARMIGHITYLSDDDMAEKFGRALRRAD 246 FNEVAR AI++DPDFHGG +Y HGV P+RGLR+ARMIGHITYLSDD M EKFGR LR Sbjct: 185 FNEVARRAIVTDPDFHGGHFYEHGVVPKRGLRIARMIGHITYLSDDVMNEKFGRELRE-- 242 Query: 247 GALDAYNFNFDVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDPAKAFNGNLSAAL 306 + Y DVEF++ESYLRYQGDKF++YFDANTYLLITRALDYFDPA G+L+AAL Sbjct: 243 -GVVRYTTQ-DVEFQIESYLRYQGDKFSEYFDANTYLLITRALDYFDPAGGHGGDLAAAL 300 Query: 307 AHTKAKYLVASFTTDWRFAPARSREIVKALLDNRRSVSYAEIDAPHGHDAFLLDDARYHN 366 A AK+L+ SF+TDWRF+P RSREIVKALLDNRRSVSYAEIDAPHGHDAFLLDD RY Sbjct: 301 ARATAKFLLVSFSTDWRFSPQRSREIVKALLDNRRSVSYAEIDAPHGHDAFLLDDVRYLG 360 Query: 367 LVRAYYERIAEEV 379 +VRA++E IA E+ Sbjct: 361 VVRAWFEGIAGEL 373 Lambda K H 0.322 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: 544 Number of extensions: 15 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: 381 Length of database: 374 Length adjustment: 30 Effective length of query: 351 Effective length of database: 344 Effective search space: 120744 Effective search space used: 120744 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 (21.9 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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