Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_010526168.1 GQW_RS0100790 homoserine O-succinyltransferase
Query= SwissProt::Q5LHS7 (305 letters) >NCBI__GCF_000220155.1:WP_010526168.1 Length = 302 Score = 401 bits (1030), Expect = e-116 Identities = 182/300 (60%), Positives = 234/300 (78%) Query: 1 MPLNLPDKLPAIELLKEENIFVIDNSRATQQDIRPLRIVILNLMPLKITTETDLVRLLSN 60 MP+N+PD LPA LL+ EN+FV+ SRA QDIRPLRI+ILNLMPLKI TET L+R+LSN Sbjct: 1 MPVNIPDLLPAKSLLEAENVFVMGESRAVTQDIRPLRILILNLMPLKIKTETHLLRVLSN 60 Query: 61 TPLQVEISFMKIKSHTSKNTPIEHMKTFYTDFDKMREDRYDGMIITGAPVEQMEFEEVNY 120 TPLQVE+ + +HT KNTP +H+ +FY FD+++ YDG IITGAPVE ++FE+V Y Sbjct: 61 TPLQVEVELLITSTHTPKNTPSQHLISFYKTFDEIKGKNYDGFIITGAPVELLDFEKVTY 120 Query: 121 WDEITEIFDWARTHVTSTLYICWAAQAGLYHHYGIPKYALDKKMFGIFKHRTLLPLHPIF 180 W+E+ +I DW++THVTSTL+ICW AQAGLYHHYGIPK+ L K+FG+F+H P P+ Sbjct: 121 WNELQKIMDWSKTHVTSTLHICWGAQAGLYHHYGIPKHELPAKLFGVFEHFVYDPTEPLV 180 Query: 181 RGFDDEFYVPHSRHTEVRKEDILKVPELTLLSESDDSGVYMVVARGGREFFVTGHSEYSP 240 RGFDD F+ PHSR+TEVRKEDI KV L LL++S+++G Y+++++ + F+TGH EY Sbjct: 181 RGFDDLFWAPHSRYTEVRKEDIEKVDNLILLADSEEAGPYIILSKDRSQVFITGHPEYDK 240 Query: 241 LTLDTEYRRDVSKGLPIEIPRNYYVNDDPDKGPLVRWRGHANLLFSNWLNYFVYQETPYN 300 LTL EY+RD KGL IP+NYY+NDDP K +VRWR HA LL+SNWLNY+VYQ TPY+ Sbjct: 241 LTLGEEYQRDQKKGLSTAIPKNYYLNDDPSKEAVVRWRSHAQLLYSNWLNYYVYQSTPYD 300 Lambda K H 0.321 0.140 0.428 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: 408 Number of extensions: 17 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: 305 Length of database: 302 Length adjustment: 27 Effective length of query: 278 Effective length of database: 275 Effective search space: 76450 Effective search space used: 76450 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: 48 (23.1 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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