Align ring 1,2-phenylacetyl-CoA epoxidase PaaC subunit (EC 1.14.13.149) (characterized)
to candidate PP_3276 PP_3276 ring 1,2-phenylacetyl-CoA epoxidase beta subunit
Query= metacyc::MONOMER-15949 (253 letters) >FitnessBrowser__Putida:PP_3276 Length = 252 Score = 395 bits (1015), Expect = e-115 Identities = 193/247 (78%), Positives = 210/247 (85%) Query: 7 LIEYLLRLGDSALIQGQRLCEWCGRAPALEEELALMNVGLDLVGQARNWLDYAAELLADG 66 LI YLL LGDSAL+QGQRLCEWCGRAPA+EEELALMNVGLDLVGQARNWL+YAAELL DG Sbjct: 6 LIPYLLLLGDSALVQGQRLCEWCGRAPAIEEELALMNVGLDLVGQARNWLEYAAELLDDG 65 Query: 67 RDADHLAFRRDERAYRNLLLVEQPNGDFAVTMAKQFLYDAWHFQVLDGLSRSGDARVAGI 126 RDAD LAFRRDERAYRNLLLVEQPNGDFAVTM KQFLYDAWHF VL GL S DAR+AGI Sbjct: 66 RDADALAFRRDERAYRNLLLVEQPNGDFAVTMTKQFLYDAWHFAVLQGLVESSDARIAGI 125 Query: 127 AAKALKEVTYHLRRSGEWVQRLGDGTEESHRRMQAAIPQLWRFTVEMSDGDEVEQRLCEA 186 AAKALKEVTYHLRRS EWVQRLG GT+ S +RM AA+P LWRFTVE++ G + E RL E Sbjct: 126 AAKALKEVTYHLRRSSEWVQRLGGGTDASRQRMLAAVPALWRFTVELAAGSDNEVRLAEC 185 Query: 187 GIAPDPAQIAGAWQAKVAEVFAAATLPLPEPAVNFYLSGRRGLHSEHLGLLLAEMQFLQR 246 GIA DPA + W +VA FA+ LPLP+ A +FYL GR+GLH+EHLGLLLAEMQFL R Sbjct: 186 GIAADPATVGATWLKQVAATFASVELPLPKAASHFYLDGRKGLHTEHLGLLLAEMQFLPR 245 Query: 247 AYPDATW 253 AYPDATW Sbjct: 246 AYPDATW 252 Lambda K H 0.321 0.136 0.421 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: 299 Number of extensions: 6 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: 253 Length of database: 252 Length adjustment: 24 Effective length of query: 229 Effective length of database: 228 Effective search space: 52212 Effective search space used: 52212 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 (21.9 bits) S2: 46 (22.3 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