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 WP_012112915.1 XAUT_RS04485 1,2-phenylacetyl-CoA epoxidase subunit A
Query= SwissProt::P76077 (309 letters) >NCBI__GCF_000017645.1:WP_012112915.1 Length = 331 Score = 447 bits (1149), Expect = e-130 Identities = 206/307 (67%), Positives = 252/307 (82%) Query: 3 QEERFEQRIAQETAIEPQDWMPDAYRKTLIRQIGQHAHSEIVGMLPEGNWITRAPTLRRK 62 Q RFE R+A E IEP D+MP AYR+TL RQI QHAHSEI+GM PEGNWITRAP+LRRK Sbjct: 22 QLARFEARVADEERIEPNDFMPAAYRRTLTRQISQHAHSEIIGMQPEGNWITRAPSLRRK 81 Query: 63 AILLAKVQDEAGHGLYLYSAAETLGCAREDIYQKMLDGRMKYSSIFNYPTLSWADIGVIG 122 A LLAKVQDE GHGLYLY+AAETLG +RE++ +++L G+ KYSSIFNYPTL+WADIG IG Sbjct: 82 AALLAKVQDECGHGLYLYAAAETLGTSREELVEQLLSGKAKYSSIFNYPTLTWADIGAIG 141 Query: 123 WLVDGAAIVNQVALCRTSYGPYARAMVKICKEESFHQRQGFEACMALAQGSEAQKQMLQD 182 WLVDGAAI+NQ+ LCR SYGPYARAM+++CKEESFHQRQG+E + LA+G+ QK+M QD Sbjct: 142 WLVDGAAIMNQIPLCRCSYGPYARAMIRVCKEESFHQRQGYEIMLTLARGTAEQKEMAQD 201 Query: 183 AINRFWWPALMMFGPNDDNSPNSARSLTWKIKRFTNDELRQRFVDNTVPQVEMLGMTVPD 242 A+NR+WWP+LMMFGP D S +S S+ WKIKRF+NDELRQ+FVD TVPQ + +T+PD Sbjct: 202 ALNRWWWPSLMMFGPPDAASSHSDSSMRWKIKRFSNDELRQKFVDATVPQAHFIDLTLPD 261 Query: 243 PDLHFDTESGHYRFGEIDWQEFNEVINGRGICNQERLDAKRKAWEEGTWVREAALAHAQK 302 PDL FD +GH+R+G IDW+EF +VI G G CN++R+ +RKA E+G WVREAA A A+K Sbjct: 262 PDLSFDEAAGHWRYGAIDWEEFKQVIAGNGPCNRDRMATRRKAHEDGAWVREAARAFAEK 321 Query: 303 QHARKVA 309 + A K A Sbjct: 322 RAAAKTA 328 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: 396 Number of extensions: 9 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: 331 Length adjustment: 28 Effective length of query: 281 Effective length of database: 303 Effective search space: 85143 Effective search space used: 85143 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 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