Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate GFF2318 Psest_2366 Homoserine acetyltransferase
Query= SwissProt::D0L1T6 (403 letters) >FitnessBrowser__psRCH2:GFF2318 Length = 340 Score = 94.0 bits (232), Expect = 6e-24 Identities = 102/340 (30%), Positives = 144/340 (42%), Gaps = 44/340 (12%) Query: 31 LALDCGRSLPSYELVYETYGQLNDEGSNAVLICHALSGDHHAAGFHAETDRKPGWWDSA- 89 + L+ G L + L Y+ G N N VLI G H W S Sbjct: 16 MRLENGERLRNARLCYQVVGTPNRARDNLVLIPSYYGGTH---------------WGSLP 60 Query: 90 -IGPGKPIDTDRFFVVCLNNLGGCKGSTGPLSVDPASGKPYGPDFPIVTVKDWVHAQYRL 148 +G P+ + VV L NL G ST P + P G DFP V++ D V AQ L Sbjct: 61 LLGADGPLAGGEYCVV-LTNLFGAGWSTSPSNAAPGQG---AADFPRVSLLDNVRAQKAL 116 Query: 149 MQYLGLSGW--AAVIGGSLGGMQVLQWSITYPDAVAHAVVIAAAPRLSAQNIAFNEVARQ 206 + L W A V G S+GGMQ L W++ YP+ V + N F E + Sbjct: 117 LDRLYGEDWQLALVTGWSMGGMQTLFWAMAYPERVRAILPFCCTAHCWPHNRVFLEGVKA 176 Query: 207 AIITDPEFYGGRYADHNALPRRGL-MLARMLGHITYLSDDAMRAKFGRELRAGQVQYGFD 265 A+ D + GGRY + P RGL R Y S R + REL GF+ Sbjct: 177 ALCADAAWLGGRY---SVPPERGLRAFGRAYAGWAY-SQAFYRQELWREL-------GFE 225 Query: 266 VEFQVESYLRYQGTSFVDRFDANTYLLMTKALDYFDPAQA-SNDDLVAALAEVKAHFLVV 324 +E+ L Y +++ DAN L + DPA++ + L AL V+A +++ Sbjct: 226 ---SLEALLDYWEQDHLEQ-DANDLLCVLHTWQSADPARSFAAGSLAEALGRVRARSILM 281 Query: 325 SFTSDWRFSPERSREIVRALLASGKQVSYAEIESNHGHDA 364 +SD F+ E +R A L G ++ +ES+ GH A Sbjct: 282 PGSSDLYFTVEDARH--EAALIPGAELRV--LESDWGHCA 317 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: 341 Number of extensions: 20 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: 403 Length of database: 340 Length adjustment: 30 Effective length of query: 373 Effective length of database: 310 Effective search space: 115630 Effective search space used: 115630 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: 49 (23.5 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