Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_028485862.1 B076_RS0102195 homoserine O-acetyltransferase
Query= SwissProt::D0L1T6 (403 letters) >NCBI__GCF_000483485.1:WP_028485862.1 Length = 386 Score = 487 bits (1253), Expect = e-142 Identities = 234/367 (63%), Positives = 286/367 (77%), Gaps = 4/367 (1%) Query: 19 IVEPKTARFSEPLALDCGRSLPSYELVYETYGQLNDEGSNAVLICHALSGDHHAAGFHAE 78 I +P+T + S PL + G LP YELVYETYG+LN + SNA+L+CHALSGDHH +G A Sbjct: 7 ITQPQTLKVSTPLEMVSGAVLPEYELVYETYGKLNADASNAILVCHALSGDHHVSGVDA- 65 Query: 79 TDRKPGWWDSAIGPGKPIDTDRFFVVCLNNLGGCKGSTGPLSVDPASGKPYGPDFPIVTV 138 D KPGWW IGPGK IDT++FFVVC NNLGGC+GSTGP S++P +G+ YGPDFPI+T Sbjct: 66 -DGKPGWWSGYIGPGKAIDTNQFFVVCSNNLGGCRGSTGPTSLNPETGQVYGPDFPIMTC 124 Query: 139 KDWVHAQYRLMQYLGLSGWAAVIGGSLGGMQVLQWSITYPDAVAHAVVIAAAPRLSAQNI 198 +DWV++Q L ++L + WAA++GGS+GGMQVLQW+I YPD + HAVVIAAAP+LSAQNI Sbjct: 125 RDWVNSQNELRKHLEIEQWAALVGGSMGGMQVLQWAIDYPDKLRHAVVIAAAPKLSAQNI 184 Query: 199 AFNEVARQAIITDPEFYGGRYADHNALPRRGLMLARMLGHITYLSDDAMRAKFGRELRAG 258 AFNEVAR+AI++DP+F+ GR+ + P++GL LARMLGH+TYLSDD M +KFGRELR Sbjct: 185 AFNEVARRAIMSDPDFHDGRFIEAGTTPKQGLALARMLGHLTYLSDDMMGSKFGRELRED 244 Query: 259 QVQYGFDVEFQVESYLRYQGTSFVDR--FDANTYLLMTKALDYFDPAQASNDDLVAALAE 316 ++QY + VEFQVESYLRYQG F + FDANTYLLMTKALDYFDPA + DL AL++ Sbjct: 245 KLQYNYGVEFQVESYLRYQGEKFATKQNFDANTYLLMTKALDYFDPASEFDHDLSKALSQ 304 Query: 317 VKAHFLVVSFTSDWRFSPERSREIVRALLASGKQVSYAEIESNHGHDAFLMTIPYYHRVL 376 A FLVVSFTSDWRFSP RS EIV+ALL + VSYAEI S HGHDAFL+ P+Y V Sbjct: 305 ACAKFLVVSFTSDWRFSPARSHEIVKALLDNDADVSYAEISSEHGHDAFLLPNPHYQGVF 364 Query: 377 AGYMANI 383 YM + Sbjct: 365 KAYMQRV 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: 541 Number of extensions: 18 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: 386 Length adjustment: 31 Effective length of query: 372 Effective length of database: 355 Effective search space: 132060 Effective search space used: 132060 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