Align ring 1,2-phenylacetyl-CoA epoxidase PaaE subunit (EC 1.14.13.149) (characterized)
to candidate WP_038218194.1 Q392_RS30125 phenylacetate-CoA oxygenase/reductase subunit PaaK
Query= metacyc::MONOMER-15950 (357 letters) >NCBI__GCF_000745855.1:WP_038218194.1 Length = 364 Score = 335 bits (859), Expect = 1e-96 Identities = 168/359 (46%), Positives = 232/359 (64%), Gaps = 6/359 (1%) Query: 4 FHSLTIKEVRPETRDAVSIAFDVPAELADSFRFTQGQHLVMRTQLDGEEVRRSYSICTGV 63 FHSL +K + P+T++AV ++F+VP +L ++F FTQGQ+L R Q++G+++RRSYSIC GV Sbjct: 5 FHSLKVKAIEPDTQEAVVVSFEVPPDLRETFGFTQGQYLTPRKQIEGQDLRRSYSICAGV 64 Query: 64 NDGELRVAIKRVAGGRFSAYANESLKAGQRLEVMPPSGHFHVELDAARHGNYLAVAAGSG 123 +DG LRV +++V GG FS + NE L+ G + M P G F V L H ++L +A GSG Sbjct: 65 DDGVLRVGVRKVRGGVFSNWINEQLQPGDEISAMAPQGRFFVPLAPEEHRHHLGIAGGSG 124 Query: 124 ITPILSIIKTTLETEPHSRVTLLYGNRSSASTLFREQLEDLKNRYLQRLNLIFLFSREQQ 183 ITPILSI+KT L EP SR TL+YGNR ST+F+E+LEDLKNRYL RL L +FS E Sbjct: 125 ITPILSIMKTVLAREPGSRFTLIYGNRHLRSTMFKEELEDLKNRYLTRLVLHHVFSDEHT 184 Query: 184 DVDLYNGRIDADKCGQLFSRWIDVKALDAAFICGPQAMTETVRDQLKANGMAAERIHFEL 243 D + G +D +K G S + +D A+ICGP M + L+A G+ IH E Sbjct: 185 DAPINMGVLDREKIGDFLSTLVPAWTIDHAYICGPFQMNDEAEAALRAAGVPESAIHIER 244 Query: 244 FAAAGSAQKREA------RESAAQDSSVSQITVISDGRELSFELPRNSQSILDAGNAQGA 297 F A +A A E+ D+ ++I ++ DG E R+ SILD +A G Sbjct: 245 FGIAQAAPGAPAGIGAVMHEARPGDAERARIVIVRDGLRREIEFHRDQPSILDCASAAGL 304 Query: 298 ELPYSCKAGVCSTCKCKVVEGEVEMDSNFALEDYEVAAGYVLSCQTFPISDKVVLDFDQ 356 E+PYSC +GVC TC+ KV+EG+V M+ NFAL+ EVAAG+VL+CQ P +++VVL FD+ Sbjct: 305 EVPYSCTSGVCGTCRSKVLEGDVRMERNFALDKAEVAAGFVLTCQAHPTTERVVLSFDE 363 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: 325 Number of extensions: 8 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: 364 Length adjustment: 29 Effective length of query: 328 Effective length of database: 335 Effective search space: 109880 Effective search space used: 109880 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 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