Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_013644807.1 METBO_RS06075 homoserine O-acetyltransferase
Query= SwissProt::D0L1T6 (403 letters) >NCBI__GCF_000191585.1:WP_013644807.1 Length = 489 Score = 389 bits (998), Expect = e-112 Identities = 195/371 (52%), Positives = 263/371 (70%), Gaps = 7/371 (1%) Query: 14 SRSVGIVEPKTARFSEPLALDCGRSLPSYELVYETYGQLNDEGSNAVLICHALSGDHHAA 73 + S+GIVE K S+ L L+ G L + ++ YETYG+LN E SNA+L+CHAL+GD H A Sbjct: 3 NESIGIVETKYHSLSDDLILESGEKLKNVQVAYETYGKLNKEKSNAILVCHALTGDAHVA 62 Query: 74 GFHAETDRKPGWWDSAIGPGKPIDTDRFFVVCLNNLGGCKGSTGPLSVDPASGKPYGPDF 133 G++ E D+KPGWWD IGPGK +DT+++F++C N +GGCKGSTGP S++P + KPYG DF Sbjct: 63 GWY-EGDKKPGWWDVIIGPGKCLDTEKYFIICSNVIGGCKGSTGPSSINPETNKPYGLDF 121 Query: 134 PIVTVKDWVHAQYRLMQYLGLSGWAAVIGGSLGGMQVLQWSITYPDAVAHAVVIAAAPRL 193 PI+T+KD V+AQ +L+ +G++ AVIGGS+GGMQVLQW ++YPD V A+ IA Sbjct: 122 PIITIKDMVNAQKKLVNSMGVTQLFAVIGGSMGGMQVLQWCVSYPDMVRSAIPIATTAFS 181 Query: 194 SAQNIAFNEVARQAIITDPEFYGGRYADHNALPRRGLMLARMLGHITYLSDDAMRAKFGR 253 S Q IAFNEV R+AII+DP + G+Y D + +P GL LARM+ HITYLS+++M KFGR Sbjct: 182 SPQQIAFNEVGRRAIISDPNWNNGQYYD-SEVPTEGLALARMIAHITYLSNESMYQKFGR 240 Query: 254 ELRAGQVQYGFDVE--FQVESYLRYQGTSFVDRFDANTYLLMTKALDYFDPAQASNDDLV 311 L+ + YGFD E F+VESYL YQG SF RFDAN+YL +TKA+DYFD A L Sbjct: 241 RLQ-DKEDYGFDFETDFEVESYLHYQGNSFTKRFDANSYLYITKAVDYFD--LAGEGSLA 297 Query: 312 AALAEVKAHFLVVSFTSDWRFSPERSREIVRALLASGKQVSYAEIESNHGHDAFLMTIPY 371 +K FLV+S SDW + P SR+IV L A+ VSY EI+S++GHDAFL+ Sbjct: 298 ETFYGLKIKFLVISVDSDWLYPPSLSRDIVMGLNANDINVSYCEIKSSYGHDAFLIEAGQ 357 Query: 372 YHRVLAGYMAN 382 + ++AG++++ Sbjct: 358 LNYLIAGFLSD 368 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: 557 Number of extensions: 27 Number of successful extensions: 5 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: 489 Length adjustment: 32 Effective length of query: 371 Effective length of database: 457 Effective search space: 169547 Effective search space used: 169547 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: 51 (24.3 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