Align ring 1,2-phenylacetyl-CoA epoxidase PaaB subunit (EC 1.14.13.149) (characterized)
to candidate YP_001312886.1 Smed_4148 phenylacetate-CoA oxygenase subunit PaaB
Query= metacyc::MONOMER-15948 (93 letters) >NCBI__GCF_000017145.1:YP_001312886.1 Length = 94 Score = 137 bits (345), Expect = 3e-38 Identities = 61/92 (66%), Positives = 77/92 (83%) Query: 2 SEWTLFEVFVRSKHGLNHKHVGSVHAADAAMAIDNARELYTRRNEGVSLWVVPSALITAS 61 SEW L+EVF+R +HGLNH+HVGS+HA DA MAI+NAR++Y RRNEGVS+WVV S I AS Sbjct: 3 SEWPLWEVFIRGQHGLNHRHVGSLHAPDAEMAINNARDVYVRRNEGVSIWVVRSIDIVAS 62 Query: 62 SPDEKEPLFDPAQDKVYRHASFYELPAEVGHM 93 +P EK PLF+P+ KVYRH +F+++P EVGHM Sbjct: 63 APSEKGPLFEPSNAKVYRHPTFFDIPDEVGHM 94 Lambda K H 0.318 0.130 0.395 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: 69 Number of extensions: 2 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: 93 Length of database: 94 Length adjustment: 10 Effective length of query: 83 Effective length of database: 84 Effective search space: 6972 Effective search space used: 6972 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: 39 (20.8 bits) S2: 39 (19.6 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 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