Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_015817511.1 TERTU_RS00980 homoserine O-acetyltransferase
Query= SwissProt::Q88CT3 (379 letters) >NCBI__GCF_000023025.1:WP_015817511.1 Length = 383 Score = 517 bits (1331), Expect = e-151 Identities = 244/381 (64%), Positives = 299/381 (78%), Gaps = 2/381 (0%) Query: 1 MSTVFPEDSVGLVVPQTARFDEPLALACGRSLASYELVYETYGTLNASASNAVLICHALS 60 M P +SVGLV PQ +FDEPLALACGR+L SY+L+ ETYGTLNAS +NA+LICHALS Sbjct: 1 MPDSIPANSVGLVTPQLMQFDEPLALACGRTLDSYQLMVETYGTLNASRTNALLICHALS 60 Query: 61 GHHHAAGYHAATDRKPGWWDSCIGPGKPIDTNRFFVVSLNNLGGCNGSTGPSSVNPATGK 120 GHHHAAGYH+ +RKPGWWD+ IGPGKP+DTN+FF+VSLNN+GGC+GSTGP + NP+TG+ Sbjct: 61 GHHHAAGYHSMDERKPGWWDAYIGPGKPLDTNKFFIVSLNNIGGCHGSTGPVTPNPSTGQ 120 Query: 121 PYGADFPVLTVEDWVHSQVRLGERLGIQQWAAVVGGSLGGMQALQWTISYPERVRHCVDI 180 P+G DFP L V DWVHSQ RL + LGIQ+WAAVVGGSLGGMQA++W++ YP+RV HCV I Sbjct: 121 PWGGDFPTLRVRDWVHSQARLADALGIQKWAAVVGGSLGGMQAMRWSLEYPDRVGHCVVI 180 Query: 181 ASAPKLSAQNIAFNEVARQAILTDPEFHGGSFQDQGVIPKRGLMLARMVGHITYLSDDSM 240 ASA KLSAQNIAFN AR+AILTDP+FH G+F +PKRGL AR++ H+TYLSDD M Sbjct: 181 ASAMKLSAQNIAFNHAAREAILTDPDFHDGNFLSHSTVPKRGLSTARVIAHLTYLSDDGM 240 Query: 241 GEKFGRELKSDKLNYDFHS-VEFQVESYLRYQGEEFSGRFDANTYLLMTKALDYFDPAAT 299 G+KFGREL+S VEFQ+ESYLRYQ + FS FDANTY+LMT+ALDYFD A Sbjct: 241 GQKFGRELRSGSFEQGTEEPVEFQIESYLRYQADSFSKVFDANTYVLMTRALDYFDLARE 300 Query: 300 HGGDLAATLAHVTADYCIMSFTTDWRFSPARSREIVDALMAARKNVCYLEIDSPYGHDAF 359 +G D Y ++SFT+DWRFSP RSREIV+AL+ A ++V Y E++S +GHDAF Sbjct: 301 YGDDPVEAFKQAQCKYMVISFTSDWRFSPERSREIVNALIRADRDVVYGELESDFGHDAF 360 Query: 360 LIPT-PRYMQGFSNYMNRIAI 379 LIP PRY ++YM++I + Sbjct: 361 LIPNQPRYWDLLTSYMSQIEV 381 Lambda K H 0.320 0.136 0.421 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: 509 Number of extensions: 19 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: 379 Length of database: 383 Length adjustment: 30 Effective length of query: 349 Effective length of database: 353 Effective search space: 123197 Effective search space used: 123197 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 (21.8 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