Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_019557573.1 F612_RS0109700 homoserine O-acetyltransferase
Query= SwissProt::D0L1T6 (403 letters) >NCBI__GCF_000381085.1:WP_019557573.1 Length = 390 Score = 497 bits (1279), Expect = e-145 Identities = 235/375 (62%), Positives = 288/375 (76%), Gaps = 4/375 (1%) Query: 17 VGIVEPKTARFSEPLALDCGRSLPSYELVYETYGQLNDEGSNAVLICHALSGDHHAAGFH 76 +G++ P+T +PL L G LP Y+L+YETYGQLN SN +LICHALSGDHH AG Sbjct: 5 LGVITPQTLHIEQPLTLSSGSILPRYDLIYETYGQLNASASNGILICHALSGDHHVAGLD 64 Query: 77 AETDRKPGWWDSAIGPGKPIDTDRFFVVCLNNLGGCKGSTGPLSVDPASGKPYGPDFPIV 136 A + KPGWW+ IGPGKPIDTD FFVVC NNLGGC GSTGP +++P +GK YGPDFPIV Sbjct: 65 A--NNKPGWWNDYIGPGKPIDTDHFFVVCSNNLGGCHGSTGPTTLNPETGKVYGPDFPIV 122 Query: 137 TVKDWVHAQYRLMQYLGLSGWAAVIGGSLGGMQVLQWSITYPDAVAHAVVIAAAPRLSAQ 196 T +DWV++Q L ++LG++ WAA+IGGS+GGMQVLQW+I YPD + HA+VIAAAP+LSAQ Sbjct: 123 TCRDWVNSQNELRKHLGINQWAALIGGSMGGMQVLQWAIDYPDKLQHAIVIAAAPKLSAQ 182 Query: 197 NIAFNEVARQAIITDPEFYGGRYADHNALPRRGLMLARMLGHITYLSDDAMRAKFGRELR 256 NIAFNEVAR+AI+TDP+F+ GR+ +H +P++GL ARMLGH+TYLSDD M AKFGRE R Sbjct: 183 NIAFNEVARRAIMTDPDFHEGRFLEHKTVPKQGLAQARMLGHLTYLSDDMMGAKFGRERR 242 Query: 257 AGQVQYGFDVEFQVESYLRYQGTSF--VDRFDANTYLLMTKALDYFDPAQASNDDLVAAL 314 ++QY ++VEFQVESYLRYQG F FDANTYLLMTKALDYFDPA + DL L Sbjct: 243 KDELQYNYEVEFQVESYLRYQGEKFATTQNFDANTYLLMTKALDYFDPASEFDHDLSKTL 302 Query: 315 AEVKAHFLVVSFTSDWRFSPERSREIVRALLASGKQVSYAEIESNHGHDAFLMTIPYYHR 374 A+ A FLV++FT+DWRF+P RS EIV+ALL + VSYAE+ES HGHDAFL+ +Y Sbjct: 303 AQTTAKFLVIAFTTDWRFAPARSHEIVKALLDNDTDVSYAEVESEHGHDAFLLRNEHYEG 362 Query: 375 VLAGYMANIDFASTP 389 + YM I TP Sbjct: 363 LFRAYMQRIISEITP 377 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: 523 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: 390 Length adjustment: 31 Effective length of query: 372 Effective length of database: 359 Effective search space: 133548 Effective search space used: 133548 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