Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_011778808.1 MVAN_RS07820 homoserine O-acetyltransferase
Query= SwissProt::A9I0E6 (424 letters) >NCBI__GCF_000015305.1:WP_011778808.1 Length = 375 Score = 238 bits (606), Expect = 3e-67 Identities = 136/364 (37%), Positives = 195/364 (53%), Gaps = 18/364 (4%) Query: 39 PLPLASGQSLQSYELAVETYGTLNAGRTNAVLVCHALNASHHVAGLAADDPNDVGWWDNM 98 PL L +G+ + +AV+ +G L+A R N V+V HAL H+ G A D GWWD + Sbjct: 26 PLTLENGEVIDDVSIAVQRWGELSARRDNVVVVLHALTGDSHITGPAGPDHPTPGWWDGV 85 Query: 99 VGPGKPLDTNRFFVIGVNNLGSCFGSTGPASINPATGHPWGAAFPVLTVEDWVHAQARLA 158 GPG P+DT+R+ I N LG C GSTGP+S+ P G WG+ FP +++ D V A Sbjct: 86 AGPGAPIDTDRWCAISTNVLGGCRGSTGPSSLAP-DGKAWGSRFPTISIRDQVAADVAAL 144 Query: 159 DHFGIERFAAVMGGSLGGMQALSWAITCPERVAHCIVIASTPRLSAQNIGFNEVARRAII 218 + FGI AAV+GGS+GG +AL W + P+ V +V+A R +A IG AI Sbjct: 145 ERFGITEVAAVIGGSMGGARALEWMMLHPDSVRAALVLAVGARATADQIGTQCTQVAAIK 204 Query: 219 TDPDFHGGDYYAHNTVPRRGLSVARMIGHITYLSDDDMAEKFGRTQR---EPAEGGAYRY 275 +DP++ GGDY+ P GL +AR H+TY + ++ E+FG + +PA GG Y Sbjct: 205 SDPNWRGGDYHGTGRSPDHGLEIARRFAHLTYRGETELDERFGNDAQPGEDPATGGRY-- 262 Query: 276 GYDVEFEVESYLRYQGEKFSRYFDANTYLLITRALDYFDPARGTGGDLARALKPAQADFL 335 V+SYL +QG K FDA TY+ +T AL D RG GG +A AL+ + Sbjct: 263 ------SVQSYLEHQGRKLLARFDAGTYVTLTDALSSHDIGRGRGG-VAAALQSCPVPTV 315 Query: 336 LVSFSTDWRFPPERSREIVRALLK-NGSPVTYAEIDAPHGHDAFLLDDARYHAVVRGYYE 394 + ++D +P E+ L +G V +D+ GHD FL++ ++R E Sbjct: 316 VGGITSDRLYPLRLQAELAELLPGCDGLDV----VDSACGHDGFLVETDAVGKLIRRTLE 371 Query: 395 RIAR 398 AR Sbjct: 372 LAAR 375 Lambda K H 0.320 0.137 0.427 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: 438 Number of extensions: 18 Number of successful extensions: 4 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: 424 Length of database: 375 Length adjustment: 31 Effective length of query: 393 Effective length of database: 344 Effective search space: 135192 Effective search space used: 135192 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