Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_013834891.1 THICY_RS01725 homoserine O-acetyltransferase
Query= SwissProt::D0L1T6 (403 letters) >NCBI__GCF_000214825.1:WP_013834891.1 Length = 377 Score = 509 bits (1310), Expect = e-149 Identities = 247/366 (67%), Positives = 294/366 (80%), Gaps = 3/366 (0%) Query: 20 VEPKTARFSEPLALDCGRSLPSYELVYETYGQLNDEGSNAVLICHALSGDHHAAGFHAET 79 V+P+T + S PL L G LPSY+LVYETYG+LN + SNAVLICHALSGDHH G++ E Sbjct: 7 VKPQTLQVSMPLQLVSGAELPSYDLVYETYGELNADASNAVLICHALSGDHHVTGYY-EG 65 Query: 80 DRKPGWWDSAIGPGKPIDTDRFFVVCLNNLGGCKGSTGPLSVDPASGKPYGPDFPIVTVK 139 D KPGWW IGPGKP+DT+ FFVVC NNLGGC+GS+GP S++PA+GK YGPDFPIVT + Sbjct: 66 DTKPGWWSDYIGPGKPVDTNEFFVVCSNNLGGCRGSSGPASLNPATGKVYGPDFPIVTCR 125 Query: 140 DWVHAQYRLMQYLGLSGWAAVIGGSLGGMQVLQWSITYPDAVAHAVVIAAAPRLSAQNIA 199 DWV++Q L Q+LG+ WAAVIGGS+GGMQV+QW+I +PD + HA+VIAAAP+LSAQNIA Sbjct: 126 DWVNSQNTLRQHLGIEQWAAVIGGSMGGMQVMQWAIDHPDKLRHALVIAAAPKLSAQNIA 185 Query: 200 FNEVARQAIITDPEFYGGRYADHNALPRRGLMLARMLGHITYLSDDAMRAKFGRELRAGQ 259 FNEVAR+AI+TDPEF GGR+ + P+ GL LARMLGH+TYLSDD M AKFGRELR+ Sbjct: 186 FNEVARRAIMTDPEFNGGRFIEAGTTPKGGLALARMLGHLTYLSDDMMGAKFGRELRSES 245 Query: 260 VQYGFDVEFQVESYLRYQGTSFVDR--FDANTYLLMTKALDYFDPAQASNDDLVAALAEV 317 ++Y FDVEFQVESYLRYQG F + FDANTYLLMTKALDYFDPA +++L AA A+ Sbjct: 246 LKYSFDVEFQVESYLRYQGEKFATKQNFDANTYLLMTKALDYFDPAAEFDNNLSAAFAQT 305 Query: 318 KAHFLVVSFTSDWRFSPERSREIVRALLASGKQVSYAEIESNHGHDAFLMTIPYYHRVLA 377 +A FLVVSFTSDWRFSP RSREIVRALL + + VSYAEIES HGHDAFL+ +Y + Sbjct: 306 QASFLVVSFTSDWRFSPTRSREIVRALLDNDRAVSYAEIESEHGHDAFLLPNTHYEGIFR 365 Query: 378 GYMANI 383 YM I Sbjct: 366 AYMNRI 371 Lambda K H 0.320 0.135 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: 539 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: 403 Length of database: 377 Length adjustment: 30 Effective length of query: 373 Effective length of database: 347 Effective search space: 129431 Effective search space used: 129431 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: 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