Align ring 1,2-phenylacetyl-CoA epoxidase PaaE subunit (EC 1.14.13.149) (characterized)
to candidate GFF2757 HP15_2701 phenylacetic acid degradation oxidoreductase PaaK
Query= metacyc::MONOMER-15950 (357 letters) >FitnessBrowser__Marino:GFF2757 Length = 359 Score = 518 bits (1335), Expect = e-152 Identities = 251/359 (69%), Positives = 303/359 (84%), Gaps = 2/359 (0%) Query: 1 MSKFHSLTIKEVRPETRDAVSIAFDVPAELADSFRFTQGQHLVMRTQLDGEEVRRSYSIC 60 M+KF+SLT+KEVRPETR+AVS+AFDVP +LAD F + QGQHL++RT+LDGEEVRRSYSIC Sbjct: 1 MNKFYSLTLKEVRPETRNAVSLAFDVPEDLADKFHYQQGQHLIVRTKLDGEEVRRSYSIC 60 Query: 61 TGVNDGELRVAIKRVAGGRFSAYANESLKAGQRLEVMPPSGHFHVELDAARHGNYLAVAA 120 VND ELR+A+K+V GGRFS +ANE LK GQ LEVMPP GHF V+LD R GNYLAVAA Sbjct: 61 RSVNDQELRIAVKQVPGGRFSTFANEQLKPGQTLEVMPPQGHFSVDLDPEREGNYLAVAA 120 Query: 121 GSGITPILSIIKTTLETEPHSRVTLLYGNRSSASTLFREQLEDLKNRYLQRLNLIFLFSR 180 GSGITPILSI+KTTLETEP S VTL YGN++++ST+FR++L+DLKN Y+ RLNL+++F+R Sbjct: 121 GSGITPILSIVKTTLETEPKSEVTLFYGNKATSSTMFRDELQDLKNEYMSRLNLVYIFTR 180 Query: 181 EQQDVDLYNGRIDADKCGQLFSRWIDVKALDAAFICGPQAMTETVRDQLKANGMAAERIH 240 E+QD+DLYNGRID +KC +LF WI+ K L AAFICGPQ MTETVRD L +GM RIH Sbjct: 181 EEQDIDLYNGRIDHEKCDKLFDHWINAKELTAAFICGPQMMTETVRDSLLNHGMEKSRIH 240 Query: 241 FELFAAAGSA-QKREARESAAQD-SSVSQITVISDGRELSFELPRNSQSILDAGNAQGAE 298 FELF AG Q R+ R+ A D S+S++TVI+DGR L+F L R+++SILDAGN +GA+ Sbjct: 241 FELFTPAGGVPQARKDRDPAHVDPQSISEVTVIADGRSLTFPLVRDTKSILDAGNEEGAD 300 Query: 299 LPYSCKAGVCSTCKCKVVEGEVEMDSNFALEDYEVAAGYVLSCQTFPISDKVVLDFDQI 357 LPYSCKAGVCSTC+ KVVEGEVEMD NFALEDYEV AGYVLSCQ +PISDKVVLD+D++ Sbjct: 301 LPYSCKAGVCSTCRAKVVEGEVEMDQNFALEDYEVEAGYVLSCQCYPISDKVVLDYDEM 359 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: 429 Number of extensions: 12 Number of successful extensions: 3 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: 359 Length adjustment: 29 Effective length of query: 328 Effective length of database: 330 Effective search space: 108240 Effective search space used: 108240 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