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_083931444.1 A3OQ_RS0101625 homoserine O-acetyltransferase
Query= SwissProt::A0A0I9RJ56 (370 letters) >NCBI__GCF_000385335.1:WP_083931444.1 Length = 449 Score = 249 bits (637), Expect = 8e-71 Identities = 146/355 (41%), Positives = 196/355 (55%), Gaps = 4/355 (1%) Query: 17 PFPFKRGGALHGARVAYETWGTLAADASNAILIVTGLSPDAHAA-ANDANPAAGWWEGMV 75 P G L VAY+T+GTL A SNAIL+ L+ D H A + GWWE MV Sbjct: 82 PLKMDAGVLLSPLTVAYQTYGTLNAQKSNAILVCHALTGDQHVANTHPVTGKPGWWEIMV 141 Query: 76 GPGKAIDTDRWFVVCVNSLGSCRGSTGPASLNPATGQPYRLDFPELSIEDGARAAIEVVR 135 GPG+ IDTDR+FV+ N +G C G+TGP+S NPATG+ Y LD P ++I+D RA +V Sbjct: 142 GPGRPIDTDRYFVISSNVVGGCMGTTGPSSTNPATGRAYGLDLPVVTIKDMVRAQAMLVD 201 Query: 136 AQGIEQLACVVGNSMGGMTALAVLMLHPGIARSHVNISGSAQALPFSIAIRSLQREAIRL 195 GI+ L CVVG SMGGM L +P + + I+ +A+ +IA + R+AI Sbjct: 202 HLGIDTLCCVVGGSMGGMQVLQWAASYPERVFAAMPIATAARHSSQNIAFHEVGRQAIMA 261 Query: 196 DPRWNGGHY-DDDAYPESGMRMARKLGVITYRSALEWDGRFGRVRLDSDQTDDDPFGLEF 254 DP W G Y D+ P G+ +AR ITY S +FGR +L F +F Sbjct: 262 DPDWCKGRYLDEGRQPTKGLAVARMAAHITYMSDEALQRKFGR-KLQDRIAPTFSFDADF 320 Query: 255 QVESYLEGHARRFVRFFDPNCYLYLSRSMDWFDLAEYADGDVLAGLAKIRVEKALAIGAN 314 Q+E+YL FV FD N YLY++R+ D+FDLAE G LA K + + N Sbjct: 321 QIENYLRYQGSSFVDRFDANSYLYVTRACDYFDLAEDYGGS-LALAFKGSKTRFCVVSFN 379 Query: 315 TDILFPVQQQQQVADGLRAGGADARFIGLESPQGHDAFLVDFERFCPAVRGFLDA 369 +D L+P + + L AGGA F+ +E+ +GHDAFL+D F RGFL+A Sbjct: 380 SDWLYPTAASRAIVHALNAGGASVSFVDIETERGHDAFLLDVPDFIATTRGFLEA 434 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: 397 Number of extensions: 23 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: 449 Length adjustment: 31 Effective length of query: 339 Effective length of database: 418 Effective search space: 141702 Effective search space used: 141702 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