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_005455200.1 SACCYDRAFT_RS07935 homoserine O-acetyltransferase
Query= SwissProt::A0A0I9RJ56 (370 letters) >NCBI__GCF_000244975.1:WP_005455200.1 Length = 376 Score = 243 bits (621), Expect = 5e-69 Identities = 150/369 (40%), Positives = 212/369 (57%), Gaps = 22/369 (5%) Query: 6 PPGTRFHALPSP-FPFKRGGALHGARVAYETWGTLAADASNAILIVTGLSPDAHAAAN-- 62 PPG R P + G L G +AYETWGTL ADASNA+LI L+ D+HAA + Sbjct: 21 PPGRRQWFRPEAVLRLESGQELPGVEIAYETWGTLNADASNAVLIEHALTGDSHAAGDIE 80 Query: 63 DANPAAGWWEGMVGPGKAIDTDRWFVVCVNSLGSCRGSTGPASLNPA-TGQPYRLDFPEL 121 +P+ GWW+G++GPGKA+DTD FVV N LG C+GSTGPAS PA G+ + FP + Sbjct: 81 PGHPSPGWWDGLIGPGKALDTDELFVVVPNVLGGCQGSTGPAS--PAEDGRYWGSRFPRI 138 Query: 122 SIEDGARAAIEVVRAQGIEQLACVVGNSMGGMTALAVLMLHPGIARSHVNISGSAQALPF 181 ++ D + + A G+E+ A V+G SMGGM AL ++ P R+ + ++ A + Sbjct: 139 TVRDQVAVEVALADALGVERWAAVLGGSMGGMRALEWAVMEPSRVRALMVLASPAASSAD 198 Query: 182 SIAIRSLQREAIRLDPRWNGGHY---DDDAYPESGMRMARKLGVITYRSALEWDGRFGRV 238 IA + Q AI DP W GG Y P G+ +AR++ TYRSA E + RFGR Sbjct: 199 QIAWSAPQLHAILADPNWKGGDYHAGGPGEGPHLGLGVARRIAHATYRSAEELNERFGR- 257 Query: 239 RLDSDQTDDDPFGLEFQVESYLEGHARRFVRFFDPNCYLYLSRSMDWFDLAEYADGDVLA 298 S Q + DP F VESYL+ HA + VR FD Y+ L+RSM+ D+ G V Sbjct: 258 ---SPQGEGDP---RFAVESYLDHHADKLVRRFDAASYVLLTRSMNGHDVGR-GRGGVGE 310 Query: 299 GLAKIRVEKALAIGANTDILFPVQQQQQVADGLRAGGADARFIGLESPQGHDAFLVDFER 358 L+++ + +A+G ++D L+P Q +++ADG+ AR+ + SP GHD+FLV+ E+ Sbjct: 311 ALSRV-TARTIAVGVDSDRLYPPGQVRELADGI----PTARYAEISSPYGHDSFLVETEQ 365 Query: 359 FCPAVRGFL 367 V+ L Sbjct: 366 VATLVKELL 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: 450 Number of extensions: 27 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: 376 Length adjustment: 30 Effective length of query: 340 Effective length of database: 346 Effective search space: 117640 Effective search space used: 117640 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