Align serine O-acetyltransferase (EC 2.3.1.30) (characterized)
to candidate 8501167 DvMF_1901 transferase hexapeptide repeat containing protein (RefSeq)
Query= BRENDA::Q6F4D7 (295 letters) >FitnessBrowser__Miya:8501167 Length = 212 Score = 58.5 bits (140), Expect = 1e-13 Identities = 38/118 (32%), Positives = 62/118 (52%), Gaps = 9/118 (7%) Query: 144 LELGDDVVVHRYVFLDDIGG-IKIGDRTSLSDYVNVYSHTHHVLASPDVTLK-------E 195 LE+ ++ ++ V +D GG I++G ++ + + H+ DV + E Sbjct: 88 LEMAENAALNVNVVVDADGGHIRMGAHVTVGPGTVIRAANHN-FDRTDVPIMFQGHEYGE 146 Query: 196 TIIGSGVRITYHATVLAGVRIGDDAMVGTGAVVTKDIPPHAIALGIPARPVRYKVRHD 253 I V I + T+ GV IG A+VG GAVVTKD+ P+ + G+PARP+R + H+ Sbjct: 147 VTIEDDVWIAANCTITPGVHIGRGAVVGAGAVVTKDVEPYTVVGGVPARPLRKRGVHE 204 Lambda K H 0.321 0.142 0.437 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: 187 Number of extensions: 12 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: 295 Length of database: 212 Length adjustment: 24 Effective length of query: 271 Effective length of database: 188 Effective search space: 50948 Effective search space used: 50948 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: 46 (22.3 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