Align ring 1,2-phenylacetyl-CoA epoxidase PaaE subunit (EC 1.14.13.149) (characterized)
to candidate PP_3274 PP_3274 ring 1,2-phenylacetyl-CoA epoxidase, reductase subunit
Query= metacyc::MONOMER-15950 (357 letters) >FitnessBrowser__Putida:PP_3274 Length = 358 Score = 590 bits (1521), Expect = e-173 Identities = 296/358 (82%), Positives = 323/358 (90%), Gaps = 1/358 (0%) Query: 1 MSKFHSLTIKEVRPETRDAVSIAFDVPAELADSFRFTQGQHLVMRTQLDGEEVRRSYSIC 60 MS+FHSLTIK+VR ETRDAVSIAFDVP L FRFTQGQ+LVMRTQLD EEVRRSYSIC Sbjct: 1 MSQFHSLTIKQVRNETRDAVSIAFDVPEHLQGQFRFTQGQYLVMRTQLDNEEVRRSYSIC 60 Query: 61 TGVNDGELRVAIKRVAGGRFSAYANESLKAGQRLEVMPPSGHFHVELDAARHGNYLAVAA 120 + V DGELRVA+KRV GGRFSA+ANE LKAGQ+LEVMPPSG F V LD AR GNYL VAA Sbjct: 61 SAVQDGELRVAVKRVPGGRFSAFANEVLKAGQQLEVMPPSGSFFVPLDPARQGNYLGVAA 120 Query: 121 GSGITPILSIIKTTLETEPHSRVTLLYGNRSSASTLFREQLEDLKNRYLQRLNLIFLFSR 180 GSGITPILSII TTL +EPHSR TLLYGNRSS+ LFR++LEDLKNRYL RLNLIF+FSR Sbjct: 121 GSGITPILSIIATTLASEPHSRFTLLYGNRSSSGALFRDKLEDLKNRYLDRLNLIFVFSR 180 Query: 181 EQQDVDLYNGRIDADKCGQLFSRWIDVKALDAAFICGPQAMTETVRDQLKANGMAAERIH 240 EQQDVDLYNGRIDADKCGQLFSRW+DV LDAAFICGPQAMTETVRD L+ANGMA ERIH Sbjct: 181 EQQDVDLYNGRIDADKCGQLFSRWLDVAGLDAAFICGPQAMTETVRDSLQANGMAKERIH 240 Query: 241 FELFAAAGSAQKREARESAAQ-DSSVSQITVISDGRELSFELPRNSQSILDAGNAQGAEL 299 FELFAAAGS +REARE+A Q DS++S ITVISDGR LSF+LPRN+Q++LDAGNA GAEL Sbjct: 241 FELFAAAGSEARREAREAARQVDSALSHITVISDGRALSFDLPRNTQNVLDAGNAIGAEL 300 Query: 300 PYSCKAGVCSTCKCKVVEGEVEMDSNFALEDYEVAAGYVLSCQTFPISDKVVLDFDQI 357 PYSCKAGVCSTCKC+V+EGEVEMDSN ALEDYEVAAGYVLSCQT+P+SDKVVLDFDQ+ Sbjct: 301 PYSCKAGVCSTCKCRVIEGEVEMDSNHALEDYEVAAGYVLSCQTYPVSDKVVLDFDQL 358 Lambda K H 0.319 0.133 0.377 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: 506 Number of extensions: 11 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: 357 Length of database: 358 Length adjustment: 29 Effective length of query: 328 Effective length of database: 329 Effective search space: 107912 Effective search space used: 107912 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: 49 (23.5 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