Align Homoserine O-acetyltransferase; HAT; EC 2.3.1.31; Homoserine transacetylase; HTA (uncharacterized)
to candidate AZOBR_RS14580 AZOBR_RS14580 homoserine O-acetyltransferase
Query= curated2:Q3AAW2 (379 letters) >FitnessBrowser__azobra:AZOBR_RS14580 Length = 398 Score = 231 bits (590), Expect = 2e-65 Identities = 136/371 (36%), Positives = 201/371 (54%), Gaps = 11/371 (2%) Query: 6 GIVETKKVTFPEITLECGEKIAPVTVAYETYGELNERGDNAILILHALTGDAHVAGKHRP 65 G+VE K P T G I V + +E+YG+LN+ DN IL+ H +G++H AGK++ Sbjct: 28 GLVEKKVFEMPSYTTVGGGTIKNVRIGWESYGKLNDARDNVILVTHFFSGNSHAAGKYKM 87 Query: 66 EDKVAGWWDPMVGPGRPFDTNKYFIVCSNVLGGC------YGTTGPSSINPATGRPWGMS 119 ED G+WD ++GPG+P DT+K+FI+ S+ L TTGP+S+NP TG+P+GMS Sbjct: 88 EDPAPGYWDSIIGPGKPLDTDKFFIISSDTLVNLSPKDPTVTTTGPASVNPDTGKPYGMS 147 Query: 120 FPIITIRDMVNLQYKLVRHLGITKILAAVGGSMGGMQALEWAYMYPEMLKSVVAIATSAR 179 FP++TIRD VN+Q L+ L + + A +GGSMG +QALEW +PEM+K VVA+ A Sbjct: 148 FPVVTIRDFVNVQKALLDSLNVKSLHAVMGGSMGSLQALEWGATHPEMVKRVVAVIGGAE 207 Query: 180 LSPFGIAFNAVGREAIMTDPEWRGGNYYGFEGPKRGLALARMIGIITYKSDISW-QYRFG 238 PF I + + I DP W+GG+YYG PK GL A + + + W FG Sbjct: 208 ADPFLIGWLNLWAAPIRVDPNWQGGDYYGKAEPKAGLTEALKL-VTLHARHWKWADATFG 266 Query: 239 RTHTYETDQELFSHTSRFEIENYLYYQGDKLVKRFDANTYLYLLKAMDLHDISRGRGRYR 298 R E S +++ IE +L DAN +LYL+KA + G G Sbjct: 267 RGWAEEGKDPAASMNNQYAIEAWLDKAAAARAAVSDANHFLYLVKANQTFLVG-GGGSLD 325 Query: 299 EILKELKTPLLAIGIDTDFLYPTYQ-QKEIVEAL-KEAKKEAYYWELSSPHGHDAFLIEF 356 E L ++K P+L I D ++P + + + E L K+ Y +++ GH + Sbjct: 326 EGLAKIKAPVLLIPSADDLVFPPERAMRPLKERLEKQGIAVTYTDAITTSLGHLDGIANI 385 Query: 357 SKMAPILSNFL 367 +K +S F+ Sbjct: 386 AKAGDAISAFM 396 Lambda K H 0.321 0.139 0.426 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: 447 Number of extensions: 20 Number of successful extensions: 4 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: 379 Length of database: 398 Length adjustment: 30 Effective length of query: 349 Effective length of database: 368 Effective search space: 128432 Effective search space used: 128432 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