Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_086000550.1 PNAP_RS20445 homoserine O-acetyltransferase
Query= SwissProt::Q2T284 (381 letters) >NCBI__GCF_000015505.1:WP_086000550.1 Length = 382 Score = 540 bits (1391), Expect = e-158 Identities = 265/373 (71%), Positives = 305/373 (81%), Gaps = 8/373 (2%) Query: 6 VVAPHTMHFAEPLRLQSGSVLGNYQLVVETYGELNAARSNAVLVCHALNASHHVAGVYAD 65 V +P +MHFA+ L L+SG+ + Y L ETYG+LNA +SNAVL+CHALNASHHVAGVY D Sbjct: 8 VASPASMHFADVLPLRSGASIRAYDLSYETYGQLNADKSNAVLICHALNASHHVAGVYLD 67 Query: 66 DP-----RSTGWWDNMVGPGKPLDTNRFFVIGVNNLGSCFGSTGPMSIDPATGTPYGARF 120 + +S GWWD M+GPGKP+DTNRFFVIGVNNLGSCFGSTGPM +P T YGA F Sbjct: 68 ESGQIQKKSEGWWDTMIGPGKPVDTNRFFVIGVNNLGSCFGSTGPMQTNPDTNEVYGADF 127 Query: 121 PVVTVEDWVHAQARVADAFGIERFAAVMGGSLGGMQALAWSLLYPERVAHCIDIASTPKL 180 PVVTV+DWV AQAR+ DA GI+ AAVMGGSLGGMQAL+W+L YP RV H + +AS P L Sbjct: 128 PVVTVQDWVDAQARLLDALGIQTLAAVMGGSLGGMQALSWTLQYPGRVRHAVVVASAPNL 187 Query: 181 SAQNIAFNEVARSAILSDPDFHGGDYYAHGVKPRRGLRVARMIGHITYLSDDDMAEKFGR 240 +A+NIAFNEVAR AI++DPDFHGG +Y HGV P+RGLR+ARMIGHITYLSDD M EKFGR Sbjct: 188 TAENIAFNEVARRAIVTDPDFHGGHFYKHGVLPKRGLRIARMIGHITYLSDDVMNEKFGR 247 Query: 241 ALRRADGALDAYNFNFDVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDPAKAFNG 300 LR A G + DVEF++ESYLRYQGDKFA+YFDANTYLLITRALDYFDPA F G Sbjct: 248 QLRDAAGIKFSTQ---DVEFQIESYLRYQGDKFAEYFDANTYLLITRALDYFDPAGEFGG 304 Query: 301 NLSAALAHTKAKYLVASFTTDWRFAPARSREIVKALLDNRRSVSYAEIDAPHGHDAFLLD 360 +LS ALA AK+L+ SFTTDWRF+PARSREIVKALLDN+ VSYAEIDAPHGHDAFLLD Sbjct: 305 DLSRALAQASAKFLLVSFTTDWRFSPARSREIVKALLDNQIDVSYAEIDAPHGHDAFLLD 364 Query: 361 DARYHNLVRAYYE 373 DARY +VR+Y+E Sbjct: 365 DARYMGVVRSYFE 377 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: 539 Number of extensions: 16 Number of successful extensions: 3 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: 382 Length adjustment: 30 Effective length of query: 351 Effective length of database: 352 Effective search space: 123552 Effective search space used: 123552 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 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