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_083789799.1 TCUR_RS07155 homoserine O-acetyltransferase
Query= SwissProt::A0A0I9RJ56 (370 letters) >NCBI__GCF_000024385.1:WP_083789799.1 Length = 385 Score = 265 bits (678), Expect = 1e-75 Identities = 156/360 (43%), Positives = 218/360 (60%), Gaps = 16/360 (4%) Query: 6 PPGTR-FHALPSPFPFKRGGALHGARVAYETWGTLAADASNAILIVTGLSPDAHAA--AN 62 PPG R + L P P + GG L G R+AYETWGT A D SNA+L++ L+ D+HAA A Sbjct: 24 PPGRRQWVTLERPLPLETGGTLPGVRLAYETWGTPAPDGSNAVLVLHALTGDSHAAGPAE 83 Query: 63 DANPAAGWWEGMVGPGKAIDTDRWFVVCVNSLGSCRGSTGPASLNPATGQPYRLDFPELS 122 +P GWW+G++GPG+ +DTDR+FVV N LG C+GSTGPASL P +P+ FP ++ Sbjct: 84 PGHPTPGWWDGLIGPGRPLDTDRYFVVVPNVLGGCQGSTGPASLRPDGRRPWGGSFPYIT 143 Query: 123 IEDGARAAIEVVRAQGIEQLACVVGNSMGGMTALAVLMLHPGIARSHVNISGSAQALPFS 182 D A +++ A GI++ A VVG SMGGM AL + P + + ++ + A Sbjct: 144 QRDQVAAEVQLADALGIDRWALVVGGSMGGMRALEWAVSQPDRVAALLLLATTGAASAEQ 203 Query: 183 IAIRSLQREAIRLDPRWNGGHYDDDA---YPESGMRMARKLGVITYRSALEWDGRFGRVR 239 IA + Q +AIR DP + GG Y D A P +G+ +ARK+ +TYRS E RFGR Sbjct: 204 IAWANAQIQAIRSDPGFRGGDYYDAAPGQGPHTGLGIARKIAHVTYRSEPELRVRFGR-- 261 Query: 240 LDSDQTDDDPF-GLEFQVESYLEGHARRFVRFFDPNCYLYLSRSMDWFDLAEYADGDVLA 298 Q D+DPF G F VESYL+ HA + VR FD N Y+ L+ +M+ D+ G + A Sbjct: 262 --RPQGDEDPFRGGRFAVESYLDHHADKLVRRFDANSYIVLTETMNGHDVGR-GRGGMAA 318 Query: 299 GLAKIRVEKALAIGANTDILFPVQQQQQVADGLRAGGADARFIGLESPQGHDAFLVDFER 358 L ++ + L G ++D L+P+ QQQ++A G+ GAD R +ESP GHD FL++ E+ Sbjct: 319 ALRRV-TARTLVAGVDSDRLYPLYQQQELAAGI--PGAD-RLRVIESPAGHDGFLIEIEQ 374 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: 469 Number of extensions: 34 Number of successful extensions: 7 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: 385 Length adjustment: 30 Effective length of query: 340 Effective length of database: 355 Effective search space: 120700 Effective search space used: 120700 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