Align ring 1,2-phenylacetyl-CoA epoxidase PaaE subunit (EC 1.14.13.149) (characterized)
to candidate WP_058857311.1 AS188_RS01210 phenylacetate-CoA oxygenase/reductase subunit PaaK
Query= metacyc::MONOMER-15950 (357 letters) >NCBI__GCF_001482365.1:WP_058857311.1 Length = 388 Score = 276 bits (705), Expect = 9e-79 Identities = 156/374 (41%), Positives = 222/374 (59%), Gaps = 20/374 (5%) Query: 2 SKFHSLTIKEVRPETRDAVSIAFDVPAELADSFRFTQGQHLVMRTQLDGEEVRRSYSICT 61 + F+SL + +VR T D+V +AF VP EL + + + GQ++ +R ++ G EVRRSYSIC Sbjct: 14 ASFNSLEVSQVRRLTADSVEVAFAVPPELVEDYDYLPGQYVALRAEIGGHEVRRSYSICA 73 Query: 62 GVNDGELRVAIKRVAGGRFSAYANESLKAGQRLEVMPPSGHFHVEL-------------- 107 GE+RVAIK+ GG FS +ANE LKAG RL+VM P G F +L Sbjct: 74 EPRPGEIRVAIKKDIGGVFSTWANEQLKAGDRLDVMNPQGAFTSKLRLTSLNDPEKLAAE 133 Query: 108 DAARHGNY--LAVAAGSGITPILSIIKTTLETEPHSRVTLLYGNRSSASTLFREQLEDLK 165 + A++ + +A AAGSGITPI++I K L S L+Y NRS+ +F E+L DLK Sbjct: 134 EVAKNSSVHLVAFAAGSGITPIMAIAKAVLRASETSTFDLVYANRSAMDVMFAEELGDLK 193 Query: 166 NRYLQRLNLIFLFSREQQDVDLYNGRIDADKCGQLFSRWIDVKALDAAFICGPQAMTETV 225 ++Y RL + + SREQ+ L +GRIDADK ++ + V D F+CGP + + Sbjct: 194 DKYPSRLAVHHVLSREQRISPLMSGRIDADKLNEILDEVVQVDRTDEWFLCGPFELVQLC 253 Query: 226 RDQLKANGMAAERIHFELFAAA--GSAQKREARESAAQDSSVSQ-ITVISDGRELSFELP 282 RD L A G+ E I FELF + Q ++ R A S + I DG E P Sbjct: 254 RDTLAARGVPEESIRFELFTTGRPENPQGQQGRVVEADPSGENYGIEFTLDGLSSRIESP 313 Query: 283 RNS-QSILDAGNAQGAELPYSCKAGVCSTCKCKVVEGEVEMDSNFALEDYEVAAGYVLSC 341 +++ +++L+A ++P++C GVC TC+ KVV GE EM+ N+ALE EV AGYVL+C Sbjct: 314 KSAHETVLNAALRVRPDVPFACAGGVCGTCRAKVVSGEFEMEENYALEKDEVDAGYVLTC 373 Query: 342 QTFPISDKVVLDFD 355 QT P +D++V+DFD Sbjct: 374 QTRPTTDELVVDFD 387 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: 344 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: 388 Length adjustment: 30 Effective length of query: 327 Effective length of database: 358 Effective search space: 117066 Effective search space used: 117066 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