Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_068464883.1 APY04_RS16095 homoserine O-acetyltransferase
Query= SwissProt::D0L1T6 (403 letters) >NCBI__GCF_001541235.1:WP_068464883.1 Length = 399 Score = 397 bits (1019), Expect = e-115 Identities = 190/365 (52%), Positives = 259/365 (70%), Gaps = 5/365 (1%) Query: 29 EPLALDCGRSLPSYELVYETYGQLNDEGSNAVLICHALSGDHHAAGFHAETDRKPGWWDS 88 +PL L C + L + YETYG+LN + SNA+L+CHAL+GD + A H T +KPGWW + Sbjct: 37 QPLRLACDQLLAPISIAYETYGELNADKSNAILVCHALTGDQYVASEHPVT-KKPGWWST 95 Query: 89 AIGPGKPIDTDRFFVVCLNNLGGCKGSTGPLSVDPASGKPYGPDFPIVTVKDWVHAQYRL 148 +GPGKP+DT+R+FV+C N LGGC GSTGP S+DPA+GKPYG +FP++T+ D V+AQ RL Sbjct: 96 LVGPGKPVDTNRYFVICSNILGGCMGSTGPASIDPATGKPYGLNFPVITIGDMVNAQVRL 155 Query: 149 MQYLGLSGWAAVIGGSLGGMQVLQWSITYPDAVAHAVVIAAAPRLSAQNIAFNEVARQAI 208 + + G+ +V+GGS+GGMQVL+W+ ++ + V AV IA APR S+QNIAF+EV RQA+ Sbjct: 156 IDHFGIDQLFSVVGGSMGGMQVLEWAASHSERVFSAVPIATAPRHSSQNIAFHEVGRQAV 215 Query: 209 ITDPEFYGGRYADHNALPRRGLMLARMLGHITYLSDDAMRAKFGRELR-AGQVQYGFDVE 267 + DP++ GG Y H +PR GL +ARM HITYLS+DA+ KFGR L+ Q+ + F+ + Sbjct: 216 MADPDWCGGDYHSHGKVPRNGLSVARMAAHITYLSEDALHHKFGRNLQNRSQLTFSFNAD 275 Query: 268 FQVESYLRYQGTSFVDRFDANTYLLMTKALDYFDPAQASNDDLVAALAEVKAHFLVVSFT 327 FQVESYLR+QG++FVDRFDAN+YL +T+A+DYFD + D L A K F VVSFT Sbjct: 276 FQVESYLRHQGSTFVDRFDANSYLYITRAMDYFDLGASRGDVLANAFRGTKTRFCVVSFT 335 Query: 328 SDWRFSPERSREIVRALLASGKQVSYAEIESNHGHDAFLMTIPYYHRVLAGYMANIDFAS 387 SDW + SR IV AL A VS+ EI+S+ GHDAFL+ P + + G++++ A Sbjct: 336 SDWLYPTRESRAIVHALNAVAANVSFVEIDSDKGHDAFLLKEPEFFATIHGFLSS---AG 392 Query: 388 TPRGV 392 RG+ Sbjct: 393 VKRGL 397 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: 488 Number of extensions: 17 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: 399 Length adjustment: 31 Effective length of query: 372 Effective length of database: 368 Effective search space: 136896 Effective search space used: 136896 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