Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate Dsui_0741 Dsui_0741 homoserine O-acetyltransferase
Query= SwissProt::Q2T284 (381 letters) >FitnessBrowser__PS:Dsui_0741 Length = 375 Score = 554 bits (1428), Expect = e-162 Identities = 266/374 (71%), Positives = 310/374 (82%), Gaps = 5/374 (1%) Query: 3 SIGVVAPHTMHFAEPLRLQSGSVLGNYQLVVETYGELNAARSNAVLVCHALNASHHVAGV 62 S+GVV+P HFAEP++L SG+ L Y LV ETYG LNA RSNAVLVCHAL+ SHHVAG Sbjct: 6 SVGVVSPQRAHFAEPIQLASGATLAAYDLVYETYGRLNADRSNAVLVCHALSGSHHVAGH 65 Query: 63 YADDPRSTGWWDNMVGPGKPLDTNRFFVIGVNNLGSCFGSTGPMSIDPATGTPYGARFPV 122 YAD+P++ GWWDN+VGPGKPLDT++FFV+GVNNLG C+GSTGP SI+PATG PYGA FPV Sbjct: 66 YADNPKNVGWWDNLVGPGKPLDTDKFFVVGVNNLGGCYGSTGPGSINPATGKPYGADFPV 125 Query: 123 VTVEDWVHAQARVADAFGIERFAAVMGGSLGGMQALAWSLLYPERVAHCIDIASTPKLSA 182 VTVEDWV +QAR+AD GI ++AA++GGSLGGMQAL WSL YPERV H + IAS PKL+A Sbjct: 126 VTVEDWVESQARLADRLGINQWAAIIGGSLGGMQALQWSLEYPERVRHALVIASAPKLTA 185 Query: 183 QNIAFNEVARSAILSDPDFHGGDYYAHGVKPRRGLRVARMIGHITYLSDDDMAEKFGRAL 242 QNIAFNEVAR AIL+DPDFHGG+YY HGV P RGLR+ARM+GHITYLSDD M EKFGR L Sbjct: 186 QNIAFNEVARQAILTDPDFHGGNYYEHGVVPARGLRLARMVGHITYLSDDQMGEKFGRQL 245 Query: 243 RRADGALDAYNFNFDVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDPAKAFNGNL 302 R +G L +N+DV+FE+ESYLRYQGDKFA +FDANTYL+ T+ALDYFDPA+ F G+L Sbjct: 246 R--EGVL---KYNYDVDFEIESYLRYQGDKFAGFFDANTYLITTKALDYFDPARDFGGDL 300 Query: 303 SAALAHTKAKYLVASFTTDWRFAPARSREIVKALLDNRRSVSYAEIDAPHGHDAFLLDDA 362 AALA AK+L+ SFTTDWRFAP RSRE+V ALL N R VSYAEID GHD+FLLDDA Sbjct: 301 KAALARASAKFLLVSFTTDWRFAPERSREMVYALLHNNREVSYAEIDCNAGHDSFLLDDA 360 Query: 363 RYHNLVRAYYERIA 376 +YH ++ AY IA Sbjct: 361 QYHAVMGAYLHNIA 374 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: 558 Number of extensions: 14 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