Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_004325782.1 C665_RS18165 homoserine O-acetyltransferase
Query= SwissProt::Q2T284 (381 letters) >NCBI__GCF_000310185.1:WP_004325782.1 Length = 375 Score = 545 bits (1403), Expect = e-159 Identities = 260/374 (69%), Positives = 303/374 (81%), Gaps = 5/374 (1%) Query: 2 ESIGVVAPHTMHFAEPLRLQSGSVLGNYQLVVETYGELNAARSNAVLVCHALNASHHVAG 61 +S+GVV P F PL L+SG L NY LV ETYG LNA RSNAVLVCHAL+ SHHVAG Sbjct: 5 QSVGVVVPQRAEFTTPLALRSGGTLNNYHLVYETYGTLNADRSNAVLVCHALSGSHHVAG 64 Query: 62 VYADDPRSTGWWDNMVGPGKPLDTNRFFVIGVNNLGSCFGSTGPMSIDPATGTPYGARFP 121 YAD P + GWWDN++GPGKPLDT +FFVIGVNNLG C+GS+GP I+PATG +GA FP Sbjct: 65 TYADAPHNVGWWDNLIGPGKPLDTRKFFVIGVNNLGGCYGSSGPNQINPATGKLWGADFP 124 Query: 122 VVTVEDWVHAQARVADAFGIERFAAVMGGSLGGMQALAWSLLYPERVAHCIDIASTPKLS 181 VTVEDWV +QAR+AD GIERFAAV+GGSLGGMQA++W+L YP+RV H IA+ PKL+ Sbjct: 125 FVTVEDWVESQARLADRLGIERFAAVVGGSLGGMQAMSWALQYPDRVGHVAVIAAAPKLT 184 Query: 182 AQNIAFNEVARSAILSDPDFHGGDYYAHGVKPRRGLRVARMIGHITYLSDDDMAEKFGRA 241 AQNIAFNEVAR AILSDP+FHGG YYAHGV P RGL++ARM+GHITYLSDD MAEKFGR+ Sbjct: 185 AQNIAFNEVARQAILSDPEFHGGHYYAHGVVPTRGLKLARMVGHITYLSDDSMAEKFGRS 244 Query: 242 LRRADGALDAYNFNFDVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDPAKAFNGN 301 LR +++DVEFE+ESYLRYQGDKFA YFDANTYLL T+ALDYFDPA + G+ Sbjct: 245 LRHGRN-----TYSYDVEFEIESYLRYQGDKFAGYFDANTYLLTTKALDYFDPAFEYGGH 299 Query: 302 LSAALAHTKAKYLVASFTTDWRFAPARSREIVKALLDNRRSVSYAEIDAPHGHDAFLLDD 361 L AALA A +LV SFTTDWRF+P RSREIV ALL N+R+VSYAEID P GHD+FLLD+ Sbjct: 300 LPAALARASADFLVISFTTDWRFSPERSREIVYALLHNKRNVSYAEIDCPAGHDSFLLDE 359 Query: 362 ARYHNLVRAYYERI 375 RYH L+ A+++RI Sbjct: 360 TRYHKLLSAWFDRI 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: 547 Number of extensions: 13 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: 375 Length adjustment: 30 Effective length of query: 351 Effective length of database: 345 Effective search space: 121095 Effective search space used: 121095 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 Apr 09 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