Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate HSERO_RS00455 HSERO_RS00455 homoserine O-acetyltransferase
Query= SwissProt::Q2T284 (381 letters) >FitnessBrowser__HerbieS:HSERO_RS00455 Length = 379 Score = 590 bits (1521), Expect = e-173 Identities = 284/377 (75%), Positives = 321/377 (85%), Gaps = 5/377 (1%) Query: 3 SIGVVAPHTMHFAEPLRLQSGSVLGNYQLVVETYGELNAARSNAVLVCHALNASHHVAGV 62 SIG+V+P MHFAEPL LQ GS L +Y L ETYG LNA +SNAVLVCHALNASHHVAGV Sbjct: 2 SIGIVSPQVMHFAEPLPLQGGSALADYSLTYETYGTLNADKSNAVLVCHALNASHHVAGV 61 Query: 63 YADDPRSTGWWDNMVGPGKPLDTNRFFVIGVNNLGSCFGSTGPMSIDPATGTPYGARFPV 122 YADDP + GWWDNMVGPGK LDT+RFFVIGVNNLGSCFGSTGPM +PATG PYGA FPV Sbjct: 62 YADDPDNVGWWDNMVGPGKSLDTDRFFVIGVNNLGSCFGSTGPMHANPATGKPYGADFPV 121 Query: 123 VTVEDWVHAQARVADAFGIERFAAVMGGSLGGMQALAWSLLYPERVAHCIDIASTPKLSA 182 VTVEDWV+AQAR+AD GI FAAVMGGSLGGMQALAWS++YP+R+ HC+ IASTPKLSA Sbjct: 122 VTVEDWVNAQARLADRLGITCFAAVMGGSLGGMQALAWSMMYPDRLRHCLVIASTPKLSA 181 Query: 183 QNIAFNEVARSAILSDPDFHGGDYYAHGVKPRRGLRVARMIGHITYLSDDDMAEKFGRAL 242 QNIAFN+VAR AIL+DP +HGGD+YAHGV P+ GLRVARM+GHITYLSDDDMAEKFGR L Sbjct: 182 QNIAFNDVARQAILTDPQYHGGDFYAHGVVPKNGLRVARMVGHITYLSDDDMAEKFGRDL 241 Query: 243 RRADGALDAYNFNFDVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDPAKAFNGNL 302 R Y F + V+FE+ESYLRYQGDKF+ YFDANTYLLIT+ALDYFDPA+ F G+L Sbjct: 242 RSGQ-----YQFGYGVDFEIESYLRYQGDKFSTYFDANTYLLITKALDYFDPAREFGGDL 296 Query: 303 SAALAHTKAKYLVASFTTDWRFAPARSREIVKALLDNRRSVSYAEIDAPHGHDAFLLDDA 362 + ALA TKAK+L+ SFTTDWRF+P RSRE+V+AL+ N+R VSYAEIDAPHGHDAFLLDDA Sbjct: 297 AKALACTKAKFLLVSFTTDWRFSPERSREMVQALVANKRRVSYAEIDAPHGHDAFLLDDA 356 Query: 363 RYHNLVRAYYERIAEEV 379 RY +VR YY I E+ Sbjct: 357 RYMKVVREYYGSIWTEL 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: 596 Number of extensions: 16 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: 379 Length adjustment: 30 Effective length of query: 351 Effective length of database: 349 Effective search space: 122499 Effective search space used: 122499 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