Align 1,2-phenylacetyl-CoA epoxidase, subunit B; 1,2-phenylacetyl-CoA monooxygenase, subunit B (characterized)
to candidate 3610438 Dshi_3819 phenylacetate-CoA oxygenase, PaaH subunit (RefSeq)
Query= SwissProt::P76078 (95 letters) >FitnessBrowser__Dino:3610438 Length = 110 Score = 136 bits (343), Expect = 6e-38 Identities = 60/90 (66%), Positives = 74/90 (82%) Query: 6 WPLYEVFVRGKQGLSHRHVGSLHAADERMALENARDAYTRRSEGCSIWVVKASEIVASQP 65 WPL+EVF+RG+ GLSHRHVGSLHA DE MA+++ARD YTRR+EG SIWVV+A I AS P Sbjct: 21 WPLWEVFIRGQHGLSHRHVGSLHAPDEEMAIKHARDVYTRRNEGVSIWVVEARHIAASSP 80 Query: 66 EERGEFFDPAESKVYRHPTFYTIPDGIEHM 95 E+G ++P+ESKVYRHPTF+ IPD + M Sbjct: 81 SEKGPLYEPSESKVYRHPTFFDIPDDVGAM 110 Lambda K H 0.319 0.133 0.414 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: 93 Number of extensions: 3 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: 95 Length of database: 110 Length adjustment: 11 Effective length of query: 84 Effective length of database: 99 Effective search space: 8316 Effective search space used: 8316 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: 40 (21.3 bits) S2: 40 (20.0 bits)
This GapMind analysis is from Sep 17 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