Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_083536601.1 ACG33_RS08120 hypothetical protein
Query= SwissProt::F4QV02 (369 letters) >NCBI__GCF_001579945.1:WP_083536601.1 Length = 363 Score = 230 bits (587), Expect = 4e-65 Identities = 130/323 (40%), Positives = 178/323 (55%), Gaps = 17/323 (5%) Query: 61 LDFGGTLTQKRVIGRLHGKANAPLIVVAGGISADRYVHRTETKGLGWWSGAVGVRAPIDL 120 L FGG L V R+ G APL+ GGISA R V + GWW G +GV +DL Sbjct: 29 LTFGGRLDTVSVAWRVSGNPQAPLVAALGGISAGRAVADVDKTQKGWWGGIIGVGKALDL 88 Query: 121 TRFRVLAFDFAPEFGEDVKDAKTPL---TITTQDQARLLALLLDHLG------------- 164 +++VL DF G + +I+T DQA +L +L H+ Sbjct: 89 NQYQVLGIDFLGGSGTTTGPRPGQVDFPSISTTDQAEILRQVLAHVRQSAIPGKGASTGR 148 Query: 165 VEKVAAFIGCSYGGMIALAFGELFPDWAEQLVVVSAAHRPHPLATAWRGIQRRILQLGLE 224 + +AA IG SYGGM+ALAF + +P E++VV+SAA +PHPL+TAWR ++R +++ Sbjct: 149 IHPLAAIIGASYGGMVALAFAQRWPQLVERIVVISAADQPHPLSTAWRSVERAVVRYATA 208 Query: 225 TGRIDQAVGLARELAMTTYRTQEEFGDRFDSEAPSHAGQ-AYPVCDYLQARGRAYRDRTT 283 G + + LAR LAMTTYR+ EF DRFD A G+ +PV YL ARG AY Sbjct: 209 RGDGPEGLRLARALAMTTYRSAREFADRFDQPAVRIDGRYQFPVESYLLARGDAYAANYI 268 Query: 284 PSRWLSLSDSIDRHRVEPEAITAPVTLIGFTTDRLCPIEDMRELADRLPNLWRFEQHASV 343 P ++ LS+SID HR++ + TL+G D+L PI DMR L RL R + +S+ Sbjct: 269 PEAFVCLSESIDLHRIDASQVRVSTTLVGIVEDQLVPIADMRRLQQRLGGPVRLVELSSL 328 Query: 344 YGHDAFLKEDKLVADILTSVLKD 366 YGHDAFLKE + + + L D Sbjct: 329 YGHDAFLKETDALRQVFAAALND 351 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: 354 Number of extensions: 12 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: 363 Length adjustment: 30 Effective length of query: 339 Effective length of database: 333 Effective search space: 112887 Effective search space used: 112887 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 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