Align Homoserine O-acetyltransferase; HAT; EC 2.3.1.31; Homoserine transacetylase; HTA (uncharacterized)
to candidate WP_020564901.1 A3OW_RS0118260 homoserine O-succinyltransferase
Query= curated2:C4Z0T6 (310 letters) >NCBI__GCF_000372865.1:WP_020564901.1 Length = 354 Score = 166 bits (420), Expect = 7e-46 Identities = 112/339 (33%), Positives = 172/339 (50%), Gaps = 41/339 (12%) Query: 1 MPIKIQSDLPAKAELEEENIFVMDENRAISQNIRPLEIIVLNLMP--IKQDTELQLLR-- 56 MP+ ++LP L EE ++ +RA Q+IR + I +LN+MP + TE Q R Sbjct: 1 MPLVAHTELPTFQRLREEGETILAPDRASHQDIREMHIGLLNIMPDAALEATERQFFRLV 60 Query: 57 GLSNTPLQIDVTFLQMSSHVSKNTSASHIKKFYQTFEEIKNNNYDGMIITGAPVEKLDFE 116 G N Q V + + + +HI K+Y+ FE+IK + D +II+GA V + + Sbjct: 61 GACNQIAQFHVHPFTIDGLPRSDAAKAHIAKYYEPFEKIKEDGLDALIISGANVTRPHLQ 120 Query: 117 EVNYWDELITVMEWSNKHVTSTIHICWGAQAGLYYHYGIKKELLPKKLSGVYKHRVMNRK 176 E ++W L V W+ ++VTS + C A + Y YGI++ LP K GV+ H++ +R Sbjct: 121 EEDFWMPLTEVFSWAKENVTSVLCSCLATHALIQYCYGIERTRLPGKRWGVFSHKLTDRT 180 Query: 177 EPLVRGFDDVFMAPHSRYTQASRQQILDNPRLKVLADSDEAGIYI-VLGDGGKEIFVMGH 235 PLV + F PHSR+ + Q ++ LKVLA S EAG+++ V DG + +F GH Sbjct: 181 HPLVAEINTRFDVPHSRFNEIF-QADMERKGLKVLAVSKEAGVHLAVSSDGFRIVFFQGH 239 Query: 236 PEYDRLTLDQEYKRDI----DKGIE--PDLPVNYYPDD-----DCNRKPLLS-------- 276 PEYD ++L +EYKR++ + IE P P NY+ ++ R ++S Sbjct: 240 PEYDEISLLKEYKREVLRYYRREIEDYPPFPENYFNEEARQIFTVYRDHVVSARRNGREL 299 Query: 277 ---------------WRSHANNLYTNWLNYYVYQITPYD 300 WR A ++ NWL VYQ+T D Sbjct: 300 EPFPENRVLEHIDNTWRDTAKAVFNNWLG-KVYQLTNQD 337 Lambda K H 0.318 0.137 0.413 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: 326 Number of extensions: 20 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 310 Length of database: 354 Length adjustment: 28 Effective length of query: 282 Effective length of database: 326 Effective search space: 91932 Effective search space used: 91932 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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