Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_051241832.1 H537_RS41150 homoserine O-acetyltransferase
Query= SwissProt::Q2T284 (381 letters) >NCBI__GCF_000430725.1:WP_051241832.1 Length = 393 Score = 567 bits (1462), Expect = e-166 Identities = 275/381 (72%), Positives = 316/381 (82%), Gaps = 4/381 (1%) Query: 1 MESIGVVAPHTMHFAEPLRLQSGSVLGNYQLVVETYGELNAARSNAVLVCHALNASHHVA 60 M SIG V P MHF +PL L+SG+ L +Y L ETYG LNAARSNAVLVCHALNASHHVA Sbjct: 1 MGSIGHVTPQRMHFPQPLPLKSGAQLPDYSLTYETYGTLNAARSNAVLVCHALNASHHVA 60 Query: 61 GVYADDPRSTGWWDNMVGPGKPLDTNRFFVIGVNNLGSCFGSTGPMSIDPATGTPYGARF 120 G YA +S GWWDN++GPGKPLDTNRFFVIGVNN GSCFGSTGP ++PATG P+G+ F Sbjct: 61 GTYAGQEKSEGWWDNLIGPGKPLDTNRFFVIGVNNPGSCFGSTGPKDLNPATGQPWGSDF 120 Query: 121 PVVTVEDWVHAQARVADAFGIERFAAVMGGSLGGMQALAWSLLYPERVAHCIDIASTPKL 180 PVVTVEDWV+AQAR+ DA GIE+ AAV+GGSLGGMQAL+W++ +P+RV H + IAS P L Sbjct: 121 PVVTVEDWVNAQARLLDALGIEQLAAVIGGSLGGMQALSWTIQHPQRVRHALVIASAPNL 180 Query: 181 SAQNIAFNEVARSAILSDPDFHGGDYYAHGVKPRRGLRVARMIGHITYLSDDDMAEKFGR 240 SAQNIAFNEVAR AI +DP+FHGG +YAHGV P+RGLRVARMIGHITYLSDD M KFGR Sbjct: 181 SAQNIAFNEVARRAICTDPEFHGGHFYAHGVVPQRGLRVARMIGHITYLSDDSMEAKFGR 240 Query: 241 ALRRADGALDAYNFNFDVEFEVESYLRYQGDKFADYFDANTYLLITRALDYFDPAKAFNG 300 ALR A+ A +EF++ESYLRYQGDKF++YFDANTYLLITRALDYFDPA+ G Sbjct: 241 ALRAAELAYSTQ----QIEFQIESYLRYQGDKFSEYFDANTYLLITRALDYFDPAREHGG 296 Query: 301 NLSAALAHTKAKYLVASFTTDWRFAPARSREIVKALLDNRRSVSYAEIDAPHGHDAFLLD 360 +LSAALA AK+LV SFTTDWRF+P RSREIV+ALLDN R V+YAEIDAPHGHDAFLL+ Sbjct: 297 DLSAALAKASAKFLVVSFTTDWRFSPLRSREIVQALLDNGRDVAYAEIDAPHGHDAFLLE 356 Query: 361 DARYHNLVRAYYERIAEEVGA 381 D RYH +VRAY+ER+A E A Sbjct: 357 DPRYHGVVRAYFERVAAEAEA 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: 560 Number of extensions: 17 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: 393 Length adjustment: 30 Effective length of query: 351 Effective length of database: 363 Effective search space: 127413 Effective search space used: 127413 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