Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate Ga0059261_3109 Ga0059261_3109 Bacterial transferase hexapeptide (six repeats)
Query= BRENDA::A0A0H2UNY1 (205 letters) >FitnessBrowser__Korea:Ga0059261_3109 Length = 192 Score = 56.2 bits (134), Expect = 4e-13 Identities = 39/130 (30%), Positives = 61/130 (46%), Gaps = 25/130 (19%) Query: 60 RFWTQIEIHPGAQIDSGVFIDH----GSGLVIGETAIVEKGVLLYHGVTLGG-------- 107 R W + + PGA+I +G + G+ + IG ++ V +Y VTL Sbjct: 21 RVWHWVHVSPGARIGAGCALGQNVYVGNDVTIGNNVRIQNNVSVYDAVTLEDDVFCGPSM 80 Query: 108 ------------TGKDCGKRHPTVRKGALISAHAQVIGPVEIGENAKVGAAAVVVADVPS 155 T KD R +RKGA + A++ ++ V +GE+A VGA AVV DV Sbjct: 81 VFTNVYNPRSAVTRKD-EYRRTLIRKGATLGANSTIVCGVVVGESAFVGAGAVVNTDVKP 139 Query: 156 DVTVVGIPAK 165 ++G+PA+ Sbjct: 140 FALMLGVPAR 149 Lambda K H 0.319 0.137 0.418 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: 99 Number of extensions: 5 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: 205 Length of database: 192 Length adjustment: 20 Effective length of query: 185 Effective length of database: 172 Effective search space: 31820 Effective search space used: 31820 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 (21.7 bits) S2: 45 (21.9 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