Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_011386326.1 AMB_RS20100 homoserine O-acetyltransferase
Query= SwissProt::D0L1T6 (403 letters) >NCBI__GCF_000009985.1:WP_011386326.1 Length = 393 Score = 384 bits (986), Expect = e-111 Identities = 190/364 (52%), Positives = 250/364 (68%), Gaps = 5/364 (1%) Query: 30 PLALDCGRSLPSYELVYETYGQLNDEGSNAVLICHALSGDHHAAGFHAETDRKPGWWDSA 89 P+ LDCG L ++ Y+TYG+LN + SNA+LICHAL+GDH+ A H T KPGWW Sbjct: 26 PIRLDCGVELGPIQVAYQTYGRLNADKSNAILICHALTGDHYVADPHPIT-AKPGWWHEL 84 Query: 90 IGPGKPIDTDRFFVVCLNNLGGCKGSTGPLSVDPASGKPYGPDFPIVTVKDWVHAQYRLM 149 +GPG+ DTDR+F++C N LGGC G+TGP+ +PA+G+ +G DFP++T+ D V Q RL+ Sbjct: 85 VGPGRVFDTDRYFLICSNVLGGCMGTTGPVDENPATGQAWGLDFPVITIGDMVKVQARLV 144 Query: 150 QYLGLSGWAAVIGGSLGGMQVLQWSITYPDAVAHAVVIAAAPRLSAQNIAFNEVARQAII 209 +LG+ V+GGS+GGMQVL+W+ YP+ V A+ IA+A R SAQNIAF+EV RQAI+ Sbjct: 145 DHLGIDQLFCVVGGSMGGMQVLKWAQVYPERVFSAIPIASAARHSAQNIAFHEVGRQAIM 204 Query: 210 TDPEFYGGRYADHNALPRRGLMLARMLGHITYLSDDAMRAKFGRELR-AGQVQYGFDVEF 268 DP++ G Y P RGL +ARM HITYLS+ A+ KFGR L+ V YGFD +F Sbjct: 205 ADPDWCEGNYLQEGKRPHRGLAVARMAAHITYLSEPALHQKFGRNLQNRDTVTYGFDADF 264 Query: 269 QVESYLRYQGTSFVDRFDANTYLLMTKALDYFDPAQASNDDLVAALAEVKAHFLVVSFTS 328 QVESYLR+QG +FVDRFDAN+YL +T+A+DYFD A S L A + F VVSFTS Sbjct: 265 QVESYLRHQGNTFVDRFDANSYLYITRAMDYFDLAAESGGVLANAFRGTRTRFCVVSFTS 324 Query: 329 DWRFSPERSREIVRALLASGKQVSYAEIESNHGHDAFLMTIPYYHRVLAGYMANIDFAST 388 DW F SR +V AL A VS+ EI+S+ GHDAFL+ P +H L G+ ++ A+T Sbjct: 325 DWLFPTPESRAVVHALNAVAANVSFVEIKSDKGHDAFLLDEPEFHATLTGF---LEGAAT 381 Query: 389 PRGV 392 RG+ Sbjct: 382 HRGL 385 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: 500 Number of extensions: 16 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: 393 Length adjustment: 31 Effective length of query: 372 Effective length of database: 362 Effective search space: 134664 Effective search space used: 134664 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 09 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