Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_043702076.1 M446_RS05285 homoserine O-acetyltransferase
Query= SwissProt::D0L1T6 (403 letters) >NCBI__GCF_000019365.1:WP_043702076.1 Length = 390 Score = 374 bits (960), Expect = e-108 Identities = 182/353 (51%), Positives = 241/353 (68%), Gaps = 2/353 (0%) Query: 30 PLALDCGRSLPSYELVYETYGQLNDEGSNAVLICHALSGDHHAAGFHAETDRKPGWWDSA 89 PLA+D G +L +++ Y+T G+LN SNAVL+CHAL+GD H A H T KPGWW++ Sbjct: 31 PLAMDAGVALAPWQIAYQTVGRLNAARSNAVLVCHALTGDQHVASRHPLTG-KPGWWETV 89 Query: 90 IGPGKPIDTDRFFVVCLNNLGGCKGSTGPLSVDPASGKPYGPDFPIVTVKDWVHAQYRLM 149 +GPGKP+DTDR+FV+C N +G C G+TGP S++PA+G PYG DFP+VT++D V Q L+ Sbjct: 90 VGPGKPVDTDRYFVICANVVGSCMGTTGPASINPATGHPYGLDFPLVTIRDMVRGQAMLL 149 Query: 150 QYLGLSGWAAVIGGSLGGMQVLQWSITYPDAVAHAVVIAAAPRLSAQNIAFNEVARQAII 209 LG+ IGGS+GGMQVLQW+ +YP+ V A+ IA R SAQNIAF+EV RQA++ Sbjct: 150 DRLGIPDLFLCIGGSMGGMQVLQWAASYPERVFAAMPIATGARHSAQNIAFHEVGRQAVM 209 Query: 210 TDPEFYGGRYADHNALPRRGLMLARMLGHITYLSDDAMRAKFGRELRAGQV-QYGFDVEF 268 DP ++GGRY D P +GL +ARM HITYLS+ A+ KFGR + + FD +F Sbjct: 210 ADPAWHGGRYLDVGTRPAKGLAVARMGAHITYLSEPALHRKFGRRFQDRDAPTFSFDADF 269 Query: 269 QVESYLRYQGTSFVDRFDANTYLLMTKALDYFDPAQASNDDLVAALAEVKAHFLVVSFTS 328 Q+ESYLR+QG SFV+RFDAN YL +T+A+DYFD A L A + F V+SFTS Sbjct: 270 QIESYLRHQGISFVERFDANAYLYLTRAMDYFDLAADHGGVLANAFRGSRTRFCVMSFTS 329 Query: 329 DWRFSPERSREIVRALLASGKQVSYAEIESNHGHDAFLMTIPYYHRVLAGYMA 381 DW F SR IV AL A+ +V++ E+ES+ GHDAFL+ P G++A Sbjct: 330 DWLFPTPDSRAIVHALNAAAARVAFVEVESDKGHDAFLLDEPAMFAAACGFIA 382 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: 476 Number of extensions: 14 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: 390 Length adjustment: 31 Effective length of query: 372 Effective length of database: 359 Effective search space: 133548 Effective search space used: 133548 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