Align ring 1,2-phenylacetyl-CoA epoxidase PaaE subunit (EC 1.14.13.149) (characterized)
to candidate HSERO_RS20630 HSERO_RS20630 phenylacetic acid degradation protein
Query= metacyc::MONOMER-15950 (357 letters) >FitnessBrowser__HerbieS:HSERO_RS20630 Length = 356 Score = 416 bits (1070), Expect = e-121 Identities = 197/356 (55%), Positives = 271/356 (76%), Gaps = 2/356 (0%) Query: 1 MSKFHSLTIKEVRPETRDAVSIAFDVPAELADSFRFTQGQHLVMRTQLDGEEVRRSYSIC 60 MSKF+ LTI +V+ ETRD + ++F VPAEL D+F + QGQHL +R++++GE++RRSYSIC Sbjct: 1 MSKFYPLTISDVKQETRDTIVVSFAVPAELQDTFSYQQGQHLTLRSEINGEDLRRSYSIC 60 Query: 61 TGVNDGELRVAIKRVAGGRFSAYANESLKAGQRLEVMPPSGHFHVELDAARHGNYLAVAA 120 + V + +LRVAIKR GG FS +ANES GQR++VMPP GHF+V L+A +YLA AA Sbjct: 61 SAVQERQLRVAIKRAPGGLFSNWANESFVPGQRIDVMPPMGHFNVPLEAGNRKHYLAFAA 120 Query: 121 GSGITPILSIIKTTLETEPHSRVTLLYGNRSSASTLFREQLEDLKNRYLQRLNLIFLFSR 180 GSGITP++SIIKTTL +EPHS TL+Y NR+S+S +F+E+L DLK+ YL+R N++++ SR Sbjct: 121 GSGITPMMSIIKTTLLSEPHSHFTLVYANRASSSVIFKEELTDLKDAYLERFNVVYVMSR 180 Query: 181 EQQDVDLYNGRIDADKCGQLFSRWIDVKALDAAFICGPQAMTETVRDQLKANGMAAERIH 240 EQQDV+L+NGRID KC F+ WID+K +DAAF+CGP+ M + V L+A+G+ +I Sbjct: 181 EQQDVELFNGRIDRAKCDAFFASWIDLKDVDAAFLCGPEEMVQAVAASLQAHGLPKTQIK 240 Query: 241 FELFAAAGSAQKREARESAAQDSSVSQITVISDGRELSFELPRNSQSILDAGNAQGAELP 300 ELFAA+ + AR + ++TVI DG F + + +S+L+AG G +L Sbjct: 241 TELFAASTPPRAHAARTVVGKQE--CEVTVIVDGYHNVFTMDKEKESVLEAGLKHGIDLR 298 Query: 301 YSCKAGVCSTCKCKVVEGEVEMDSNFALEDYEVAAGYVLSCQTFPISDKVVLDFDQ 356 YSCK GVC+TC+CKVVEG+V+MD+N+ALEDYE+A G+VLSCQ+FP+SDK++LDFDQ Sbjct: 299 YSCKGGVCATCRCKVVEGKVDMDANYALEDYEIARGFVLSCQSFPVSDKLLLDFDQ 354 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: 412 Number of extensions: 24 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: 356 Length adjustment: 29 Effective length of query: 328 Effective length of database: 327 Effective search space: 107256 Effective search space used: 107256 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