Align Serine O-acetyltransferase; EC 2.3.1.30 (characterized, see rationale)
to candidate GFF220 PS417_01115 serine acetyltransferase
Query= uniprot:Q72EB6_DESVH (323 letters) >FitnessBrowser__WCS417:GFF220 Length = 308 Score = 261 bits (667), Expect = 2e-74 Identities = 133/261 (50%), Positives = 168/261 (64%) Query: 41 GSPMPSLEALTELMARLRAALFPGYFGASNIVLESMRYHLAANLDSIYRILAEQVRRGGC 100 G +PS EA+ +++ L ALFP G ++ ES +++ LD L Q R Sbjct: 37 GRELPSREAVAQILESLCGALFPMRLGPVDLREESEDFYVGHTLDVALNALLGQARLELR 96 Query: 101 FACADYATDCQNCESHSQETAMEFMRALPRIRQLLATDVKAAYEGDPAAKSPGETIFCYP 160 +A A D + + +F ALP +R LL TDV AAY GDPAA+S E + CYP Sbjct: 97 YAARQGAKDDSEVDVLAIRLIQDFALALPSLRSLLDTDVLAAYHGDPAARSVDEVLLCYP 156 Query: 161 SIYAMIHHRIAHELYRLDVPVIPRIISEMAHSRTGIDIHPGATVGEEFFIDHGTGVVIGE 220 + A+IHHR+AH LYR +P++ RI +E+AHS TGIDIHPGA +G FFIDHGTGVVIGE Sbjct: 157 GVLAVIHHRLAHHLYRAGLPLLARISAEIAHSATGIDIHPGAQIGPSFFIDHGTGVVIGE 216 Query: 221 TCIIGRGCRLYQGVTLGALSFPKDGGGALIKGIPRHPILQDGVTVYAGATILGRVTIGAG 280 T IIG R+YQ VTLGA FP D G L KG PRHPI++D V +YAGATILGR+TIG G Sbjct: 217 TAIIGERVRIYQAVTLGAKRFPADEDGQLQKGHPRHPIVEDDVVIYAGATILGRITIGKG 276 Query: 281 AIVGGNVWVTHDVAPGAKVVQ 301 + +GGNVW+T V GA + Q Sbjct: 277 STIGGNVWLTRSVPAGANITQ 297 Lambda K H 0.320 0.137 0.410 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: 349 Number of extensions: 17 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: 323 Length of database: 308 Length adjustment: 27 Effective length of query: 296 Effective length of database: 281 Effective search space: 83176 Effective search space used: 83176 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: 48 (23.1 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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