Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_077279635.1 B1C78_RS13180 homoserine O-succinyltransferase
Query= SwissProt::L0E1U3 (356 letters) >NCBI__GCF_002000365.1:WP_077279635.1 Length = 359 Score = 523 bits (1348), Expect = e-153 Identities = 249/352 (70%), Positives = 292/352 (82%) Query: 1 MPLVAHSNLPTFERLRKEGGTVLPNDYALHQDIRALHIGLLNMMPDAALAATERQFFRLV 60 MPLVAH++LPTFERL +EG T+L D A+ Q+IR LH+GLLNMMPDAA+ ATERQFFRLV Sbjct: 1 MPLVAHTDLPTFERLAQEGETILSGDTAVQQEIRELHVGLLNMMPDAAIRATERQFFRLV 60 Query: 61 GESNQIAQFYMHPFTLAELPRGPGGQAHVERYYETFDTIQREGLDALIITGANVSQPDLA 120 G+SNQIAQFYMHPFTL LPRGP G+AH+ERYYETF+ I+R+GLDALIITGANV+Q DL+ Sbjct: 61 GQSNQIAQFYMHPFTLDTLPRGPEGRAHIERYYETFEQIKRDGLDALIITGANVTQSDLS 120 Query: 121 LEPFWEPLAEVVEWAWKNVTSTLCSCLTTHAVMQSRYGERRRHRGAKLWGVFDHRVVDRT 180 LEPFWEPL EV++WA +NVTSTLCSCL THAVMQ RYG++R+ G K WGV+ HRV+DR Sbjct: 121 LEPFWEPLIEVIDWACENVTSTLCSCLATHAVMQFRYGQKRQPLGFKRWGVYPHRVLDRR 180 Query: 181 HPLVAGVNTRFDVPHSRFNDVSREQFDRHRLKVLVESERAGVHLAVSEDGFRLVFFQGHP 240 HPLV+GVNTRFDVPHSRFN++SR QF+ LKVL ES+ AG HLAVSEDG R+VFFQGHP Sbjct: 181 HPLVSGVNTRFDVPHSRFNEISRSQFEGQGLKVLAESDTAGPHLAVSEDGLRIVFFQGHP 240 Query: 241 EYDSISLLKEYKREVLRFVNGEREEFPPLPERYLSPQAAAILEEHRERVEQARQRRVPAP 300 EYD ISLLKEYKREV R+V G + +PP PE Y + ++ AIL+EHRERV+ A RR P P Sbjct: 241 EYDIISLLKEYKREVKRYVAGAIDTYPPFPEHYFTARSQAILDEHRERVQAALARRAPVP 300 Query: 301 ELPEPLLVGRLDNTWHDSALAVVNNWIGNVYQFTNHDRRIPFRPGVDPNAPL 352 ELPE L+ LDNTWHD+A AV+NNWIG VYQ T+ DRR PF+ VDP PL Sbjct: 301 ELPEALITSSLDNTWHDTAEAVINNWIGIVYQLTHIDRRRPFKNNVDPANPL 352 Lambda K H 0.322 0.138 0.429 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: 479 Number of extensions: 10 Number of successful extensions: 1 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: 356 Length of database: 359 Length adjustment: 29 Effective length of query: 327 Effective length of database: 330 Effective search space: 107910 Effective search space used: 107910 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 (21.9 bits) S2: 49 (23.5 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