Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_072906806.1 BUB13_RS06080 homoserine O-acetyltransferase
Query= SwissProt::D0L1T6 (403 letters) >NCBI__GCF_900142125.1:WP_072906806.1 Length = 373 Score = 327 bits (837), Expect = 5e-94 Identities = 167/371 (45%), Positives = 234/371 (63%), Gaps = 2/371 (0%) Query: 13 LSRSVGIVEPKTARFSEPLALDCGRSLPSYELVYETYGQLNDEGSNAVLICHALSGDHHA 72 ++ SVG+V+ + A F L L+ GR L + +E YGQLN N +L+ HA +GD HA Sbjct: 1 MNDSVGLVKTEYADFDVELRLESGRLLGPLTIAFERYGQLNAAKDNVILVTHAWTGDAHA 60 Query: 73 AGFHAETDRKPGWWDSAIGPGKPIDTDRFFVVCLNNLGGCKGSTGPLSVDPASGKPYGPD 132 AG H E DRKPGWWD+ IGPGK DTD++FV+C N +G CKGSTGP S+DP +G+PY Sbjct: 61 AGVHDEEDRKPGWWDNMIGPGKVFDTDKYFVLCSNVIGSCKGSTGPTSIDPKTGRPYRLK 120 Query: 133 FPIVTVKDWVHAQYRLMQYLGLSGWAAVIGGSLGGMQVLQWSITYPDAVAHAVVIAAAPR 192 FP + V+D V AQ L+ +LG++ AV+GGS+G MQ ++W+I YP+ + V IA R Sbjct: 121 FPSLMVRDMVRAQKLLIDHLGITSIHAVVGGSMGAMQAIEWAIHYPEMIRAIVPIAGTGR 180 Query: 193 LSAQNIAFNEVARQAIITDPEFYGGRYADHNALPRRGLMLARMLGHITYLSDDAMRAKFG 252 S IA N +ARQAI DP + G Y + P GL LAR +GHI++LSD +M KFG Sbjct: 181 TSPMAIALNALARQAIFNDPLWKKGNYRPEHP-PADGLALARAVGHISFLSDASMWLKFG 239 Query: 253 RELRAGQVQYGFDVEFQVESYLRYQGTSFVDRFDANTYLLMTKALDYFDPAQASNDDLVA 312 R + F +F++E YL Y G +FVDRFD N++L + KALD +D A + D L Sbjct: 240 RRFSVRDGMFDFFGKFEIERYLDYNGGNFVDRFDTNSFLYLAKALDLYDVAW-NFDSLSE 298 Query: 313 ALAEVKAHFLVVSFTSDWRFSPERSREIVRALLASGKQVSYAEIESNHGHDAFLMTIPYY 372 AL + L +FTSDW ++P++++E+V L K V Y IES++GHD+FL+ + Sbjct: 299 ALDRLNCPSLWFAFTSDWLYTPQQTQEVVDELRRLNKPVDYHLIESDYGHDSFLVEPEKF 358 Query: 373 HRVLAGYMANI 383 +L ++A + Sbjct: 359 IPILQTFLAEV 369 Lambda K H 0.320 0.135 0.412 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: 448 Number of extensions: 25 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: 403 Length of database: 373 Length adjustment: 30 Effective length of query: 373 Effective length of database: 343 Effective search space: 127939 Effective search space used: 127939 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