Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_092996902.1 BLP65_RS11095 homoserine O-succinyltransferase
Query= SwissProt::Q3J7P0 (358 letters) >NCBI__GCF_900102855.1:WP_092996902.1 Length = 355 Score = 535 bits (1379), Expect = e-157 Identities = 251/355 (70%), Positives = 301/355 (84%), Gaps = 1/355 (0%) Query: 1 MPLVANSDLPAFERLREEGETVIPRDVALHQDIREMHIGLLNMMPDAALAATERQFFRLI 60 MPLVAN++LPAF RLR+EG+ V+ RDVA+HQDIRE+H+GLLNMMPDAAL+ATERQFFRL+ Sbjct: 1 MPLVANTELPAFSRLRQEGQNVLERDVAVHQDIRELHVGLLNMMPDAALSATERQFFRLV 60 Query: 61 GESNQIAQFYIHPFTLKEIQRSLEANHYVERYYQTFEQIQAEGLDALIITGANVTQPQLS 120 GE+NQIAQFY+HPFTLKE++R +A +++RYY+ FE + EGLDALIITGANV +LS Sbjct: 61 GEANQIAQFYMHPFTLKELERGPDAAGHIDRYYERFEDLMDEGLDALIITGANVQGTELS 120 Query: 121 LEPFWKPLIKVISWAYENVTSTLCSCLATHAVLDFRYGQKRRRLSSKRWGVYSHRVVNRS 180 +PFWKPLI+VI WAYENVTSTLCSCL THAV++FRYGQKRR L KRWGVYSHR V+ Sbjct: 121 EQPFWKPLIRVIDWAYENVTSTLCSCLTTHAVMEFRYGQKRRPLGFKRWGVYSHR-VSGQ 179 Query: 181 HPLVRGVNTRFDVPHSRFNEISRDQFEAAGLHVLAESEKGGAHLAVSEDLFRIVFCQGHP 240 HPLV GVNTRFDVPHSRFN I R+QFE+ G VLAESE+ G HLA SEDLFR+VF QGHP Sbjct: 180 HPLVAGVNTRFDVPHSRFNAIGREQFESVGCRVLAESEEAGVHLATSEDLFRLVFFQGHP 239 Query: 241 EYDSISLLKEYKREILRFASGQRDNYPPFPENYFSPKIQAILEEYQEQIIIARDKDLPLP 300 EYD ISLLKEYKRE+ F +G+RD+YPP +NYF+P+ +AIL+E++ ++ AR++ P+P Sbjct: 240 EYDVISLLKEYKREVTLFGAGRRDDYPPSIDNYFTPQAEAILDEHRLRVSSARERGQPIP 299 Query: 301 QLPEPLIVDYLDNTWHDTAEAIINNWMGNVYQITHSDRKRPFMEDIAPDDPLGLR 355 + PE LIVDYLDNTWHDTAEAIIN W+G VYQ+TH DRKRPF E I P+DP GLR Sbjct: 300 EFPEKLIVDYLDNTWHDTAEAIINKWIGRVYQLTHHDRKRPFKEGIDPNDPFGLR 354 Lambda K H 0.321 0.137 0.416 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: 500 Number of extensions: 15 Number of successful extensions: 2 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: 358 Length of database: 355 Length adjustment: 29 Effective length of query: 329 Effective length of database: 326 Effective search space: 107254 Effective search space used: 107254 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