Align Serine O-succinyltransferase; SST; Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.-; EC 2.3.1.46 (characterized)
to candidate WP_012590062.1 MSIL_RS21000 homoserine O-acetyltransferase
Query= SwissProt::A0A0I9RJ56 (370 letters) >NCBI__GCF_000021745.1:WP_012590062.1 Length = 394 Score = 260 bits (665), Expect = 4e-74 Identities = 142/349 (40%), Positives = 198/349 (56%), Gaps = 4/349 (1%) Query: 23 GGALHGARVAYETWGTLAADASNAILIVTGLSPDAHAA-ANDANPAAGWWEGMVGPGKAI 81 GG L+ +AY+T+G L A SNAIL+ L+ D H A A+ GWW MVGPG+ I Sbjct: 36 GGRLNQWTIAYQTYGELNAAKSNAILVCHALTGDQHVANAHPVTGKPGWWSTMVGPGRPI 95 Query: 82 DTDRWFVVCVNSLGSCRGSTGPASLNPATGQPYRLDFPELSIEDGARAAIEVVRAQGIEQ 141 DTDR+FV+C N +G C G+TGPASLNP TG+PY L+ P ++I D RA ++ G++ Sbjct: 96 DTDRYFVICSNVIGGCMGTTGPASLNPQTGRPYGLELPIVTIRDMVRAQAMLIDHLGVDT 155 Query: 142 LACVVGNSMGGMTALAVLMLHPGIARSHVNISGSAQALPFSIAIRSLQREAIRLDPRWNG 201 L CVVG SMGGM L + P S + I+ +A+ +IA + R+A+ DP W Sbjct: 156 LFCVVGGSMGGMQVLQWVASFPERVFSAMPIATAAKHSSQNIAFHEVGRQAVMADPDWRK 215 Query: 202 GHY-DDDAYPESGMRMARKLGVITYRSALEWDGRFGRVRLDSDQTDDDPFGLEFQVESYL 260 G Y ++ P G+ +AR ITY S +FGR D D F EFQ+E+YL Sbjct: 216 GRYLEEGVIPTKGLAVARMAAHITYLSDEALQSKFGRKLQDRD-APTFSFDAEFQIENYL 274 Query: 261 EGHARRFVRFFDPNCYLYLSRSMDWFDLAEYADGDVLAGLAKIRVEKALAIGANTDILFP 320 FV FDPN YLY++R+ D+FDLA DG + ++ + + N+D L+P Sbjct: 275 RYQGSSFVDRFDPNSYLYVTRACDYFDLAADYDGSLARAFQGVKA-RFCVVSFNSDWLYP 333 Query: 321 VQQQQQVADGLRAGGADARFIGLESPQGHDAFLVDFERFCPAVRGFLDA 369 + + L AGGA F+ +E+ +GHDAFL+D F +GFLD+ Sbjct: 334 TAASRAIVHALNAGGASVSFVDIETDRGHDAFLLDLPEFIATSQGFLDS 382 Lambda K H 0.322 0.138 0.432 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: 380 Number of extensions: 22 Number of successful extensions: 5 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: 370 Length of database: 394 Length adjustment: 30 Effective length of query: 340 Effective length of database: 364 Effective search space: 123760 Effective search space used: 123760 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