Align 1,2-phenylacetyl-CoA epoxidase, subunit A; 1,2-phenylacetyl-CoA epoxidase, catalytic subunit alpha; 1,2-phenylacetyl-CoA monooxygenase, subunit A; EC 1.14.13.149 (characterized)
to candidate BWI76_RS13090 BWI76_RS13090 phenylacetate-CoA oxygenase subunit PaaA
Query= SwissProt::P76077 (309 letters) >FitnessBrowser__Koxy:BWI76_RS13090 Length = 309 Score = 585 bits (1508), Expect = e-172 Identities = 279/309 (90%), Positives = 291/309 (94%) Query: 1 MTQEERFEQRIAQETAIEPQDWMPDAYRKTLIRQIGQHAHSEIVGMLPEGNWITRAPTLR 60 MT+E+RFEQRIAQETAIEP DWMP+AYRKTLIRQIGQHAHSEIVGMLPEGNWI RAPTLR Sbjct: 1 MTEEQRFEQRIAQETAIEPLDWMPEAYRKTLIRQIGQHAHSEIVGMLPEGNWIARAPTLR 60 Query: 61 RKAILLAKVQDEAGHGLYLYSAAETLGCAREDIYQKMLDGRMKYSSIFNYPTLSWADIGV 120 RKAILLAKVQDEAGHGLYLYSAAETLGCARED+YQKMLDG+MKYSSIFNYPTLSWADIGV Sbjct: 61 RKAILLAKVQDEAGHGLYLYSAAETLGCAREDLYQKMLDGKMKYSSIFNYPTLSWADIGV 120 Query: 121 IGWLVDGAAIVNQVALCRTSYGPYARAMVKICKEESFHQRQGFEACMALAQGSEAQKQML 180 IGWLVDGAAIVNQVALCRTSYGPYARAMVKICKEESFHQRQGFEACMALAQGS+AQ+QML Sbjct: 121 IGWLVDGAAIVNQVALCRTSYGPYARAMVKICKEESFHQRQGFEACMALAQGSDAQRQML 180 Query: 181 QDAINRFWWPALMMFGPNDDNSPNSARSLTWKIKRFTNDELRQRFVDNTVPQVEMLGMTV 240 QDAINRFWWPALMMFGPNDDNSPNSARS+ WKIK +NDELRQRFVDNT+PQVE+LGMTV Sbjct: 181 QDAINRFWWPALMMFGPNDDNSPNSARSMAWKIKLHSNDELRQRFVDNTIPQVEILGMTV 240 Query: 241 PDPDLHFDTESGHYRFGEIDWQEFNEVINGRGICNQERLDAKRKAWEEGTWVREAALAHA 300 PDPDL D +GHYRFG IDWQEFNE I GRGICN ERL AKRKAWEEG WVREAALAHA Sbjct: 241 PDPDLRLDETTGHYRFGAIDWQEFNETIAGRGICNHERLAAKRKAWEEGAWVREAALAHA 300 Query: 301 QKQHARKVA 309 QKQ AR A Sbjct: 301 QKQRARDAA 309 Lambda K H 0.320 0.133 0.418 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: 507 Number of extensions: 10 Number of successful extensions: 1 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: 309 Length of database: 309 Length adjustment: 27 Effective length of query: 282 Effective length of database: 282 Effective search space: 79524 Effective search space used: 79524 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: 48 (23.1 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