Align Serine O-succinyltransferase; SST; Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.-; EC 2.3.1.46 (characterized)
to candidate N515DRAFT_4362 N515DRAFT_4362 homoserine O-acetyltransferase
Query= SwissProt::Q8P8L2 (380 letters) >FitnessBrowser__Dyella79:N515DRAFT_4362 Length = 339 Score = 146 bits (369), Expect = 7e-40 Identities = 123/364 (33%), Positives = 164/364 (45%), Gaps = 63/364 (17%) Query: 18 LPMKRGGVLHQARVAYETWGTLDADHGNAVLIVTGLSPNAHAAANADNPEPGWWEAMVGP 77 L K G + V Y G DA V++ G+S N A D PGWW+ VG Sbjct: 36 LSPKYGSRPCEVDVRYLWCGAPDAP---TVIVQGGISANREVVALDDEATPGWWQEAVGA 92 Query: 78 GKPIDTDRWFVVCVNSLGSCKGSTGPASIDPATGAPYRLSFPELSIEDVADAAADVVRAL 137 G+PID DR+ V+C++ L PA +D AT +S ED ADA A +V AL Sbjct: 93 GRPIDLDRYRVLCIDWLT-------PAELDGATA---------VSSEDQADALAALVEAL 136 Query: 138 GIAQLACLIGNSMGGMTALALLLRHPGIARSHINISGSAQALPFSIAIRSLQREAIRLDP 197 GIA++ IG+S G M LA RHP + ++G+ + P + A R++QR +RL Sbjct: 137 GIARVHAFIGSSYGAMAGLAFAARHPYALDRLVLLAGAHRPHPLATAQRAVQRGIVRLGV 196 Query: 198 HWNGGHYDDVQYPESGMRMARKLGVITYRSALEWDGRFGRVRLDSELTAEDPF---GLEF 254 + PE + +AR+L + TYR + E+ RF TA F F Sbjct: 197 --------ETGQPEQALSLARQLAMTTYRGSEEFSRRF---------TAAPEFREGRFHF 239 Query: 255 QVESYLEGHARRFVRFFDPNCYLYLSRSMDWFDLAEYAPDTRADAAAPESGVLAGLAQIR 314 VE YL RRFV FD +L LS S+D D+ T AAP Sbjct: 240 PVEDYLVHQGRRFVERFDVERFLALSESIDLHDV------TPERIAAP------------ 281 Query: 315 IARALAIGANTDILFPVQQQEQIAEGLRAGGADAQFLGLDSPQGHDAFLVDFARFGPAVR 374 A IG +D L P+ + E R A L+SP GHDAFL + R P +R Sbjct: 282 ---ATLIGFPSDRLVPL---SDLCELQRRLHGPATLEVLESPYGHDAFLKETHRLAPLLR 335 Query: 375 AFLA 378 LA Sbjct: 336 DALA 339 Lambda K H 0.321 0.137 0.427 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: 297 Number of extensions: 16 Number of successful extensions: 6 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: 380 Length of database: 339 Length adjustment: 29 Effective length of query: 351 Effective length of database: 310 Effective search space: 108810 Effective search space used: 108810 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 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