Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_085217919.1 B9N75_RS05680 alpha/beta fold hydrolase
Query= SwissProt::F4QV02 (369 letters) >NCBI__GCF_900177405.1:WP_085217919.1 Length = 321 Score = 204 bits (520), Expect = 2e-57 Identities = 119/293 (40%), Positives = 164/293 (55%), Gaps = 14/293 (4%) Query: 78 GKANAPLIVVAGGISADRYVHRTETKGLGWWSGAVGVRAPIDLTRFRVLAFDFAPEFGED 137 G +AP+++V GGISA+R+ G GWW G G + +D R+R+L DF D Sbjct: 37 GPESAPVVLVLGGISANRFPAVRPDGGAGWWPGVAGAGSALDPARWRILGMDFV----SD 92 Query: 138 VKDAKTPLTITTQDQARLLALLLDHLGVEKVAAFIGCSYGGMIALAFGELFPDWAEQLVV 197 + + P + D A L+A LD G+ +V A +G SYGGMIA+ F + +PD +LV Sbjct: 93 PEGRRAP---ASADVAALIAAALDAAGIARVHAAVGASYGGMIAMRFAQDYPDRCARLVA 149 Query: 198 VSAAHRPHPLATAWRGIQRRILQLGLETGRIDQAVGLARELAMTTYRTQEEFGDRFDSEA 257 +SA R HP +TA R +QRR + LGL GR +A+ +AR +AM TYRT+EEF DRF+ Sbjct: 150 ISADARAHPASTAIRELQRRTVALGLAAGRGQEALSIARGMAMLTYRTREEFADRFEG-- 207 Query: 258 PSHAGQAYPVC----DYLQARGRAYRDRTTPSRWLSLSDSIDRHRVEPEAITAPVTLIGF 313 +G C YL+ARG Y +P R+LSLS +IDRH EP I P LIG Sbjct: 208 -GISGDDVLECTQPGTYLRARGDVYHQVMSPERFLSLSAAIDRHVAEPAKIAVPSLLIGA 266 Query: 314 TTDRLCPIEDMRELADRLPNLWRFEQHASVYGHDAFLKEDKLVADILTSVLKD 366 T+D L P M LA + R S YGHD FLK+ ++ ++ L++ Sbjct: 267 TSDLLVPPSQMEALAGGIGANARLVLRHSAYGHDMFLKDADAISALIAPFLEE 319 Lambda K H 0.321 0.137 0.412 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: 338 Number of extensions: 20 Number of successful extensions: 3 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: 369 Length of database: 321 Length adjustment: 29 Effective length of query: 340 Effective length of database: 292 Effective search space: 99280 Effective search space used: 99280 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 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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