Align ring 1,2-phenylacetyl-CoA epoxidase PaaA subunit (EC 1.14.13.149) (characterized)
to candidate WP_011764039.1 AZO_RS01540 1,2-phenylacetyl-CoA epoxidase subunit A
Query= metacyc::MONOMER-15947 (330 letters) >NCBI__GCF_000061505.1:WP_011764039.1 Length = 331 Score = 444 bits (1141), Expect = e-129 Identities = 217/334 (64%), Positives = 261/334 (78%), Gaps = 8/334 (2%) Query: 1 MYAQLVETGVKRVKALEEMAPEERAFQERIDAEIK----IEAKNWMPDAYRQTLIRQISQ 56 MY Q ++ + + A A E A+Q DA I IE K+WMP+AYR+TL+RQISQ Sbjct: 1 MYTQALD--IPQADAAPLRAVENPAYQAEFDARIDAGDFIEPKDWMPEAYRKTLVRQISQ 58 Query: 57 HAHSEIVGMLPEGNWVTRAPTLKRKLQLMAKIQDEAGHGLYLYSAMETLGADRDEEIAKL 116 HAHSEIVGMLPEGNW+TRAP+LKRK L+AK+QDE GHGLYLY+A ETLG RDE L Sbjct: 59 HAHSEIVGMLPEGNWITRAPSLKRKAILLAKVQDEGGHGLYLYAAAETLGVSRDELYEAL 118 Query: 117 HSGKAKYSSIFNYPTLNWADMGAVGWLVDGAAIVNQVVLQRTSYGPYSRAMIRICKEESF 176 +G+AKYSSIFNYPTLNWAD+G +GWLVDGAAI+NQ+ L + SYGPY+RAMIR+CKEESF Sbjct: 119 LAGRAKYSSIFNYPTLNWADIGVIGWLVDGAAIMNQIPLCKCSYGPYARAMIRVCKEESF 178 Query: 177 HQRQGYEILLTMMRHGTQAQKDMVQDAINRLWWPALMMFGPSDEHSPNSAQSMAWKIKRQ 236 HQRQGY++LLTMMR GT Q++MVQDA+NR WWP++MMFGP D S ++ ++ W IKR Sbjct: 179 HQRQGYDLLLTMMR-GTPEQQEMVQDAVNRWWWPSIMMFGPHDSDSVHT-ETTRWGIKRI 236 Query: 237 SNDELRQRFIDQTVPQLELLGCTAPDPELKWNEERGHYDFGAIDWSEFYEVLKGNGPCNA 296 SND+LRQ+F+D TV Q E+LG T PDP LKWNE RGHYDFGAIDW EF V+ G+G CN Sbjct: 237 SNDDLRQKFVDATVKQAEVLGVTLPDPALKWNEARGHYDFGAIDWDEFRAVVGGHGQCNV 296 Query: 297 ERIATRRNAIDNGAWVREAAVAHARKQQHKRDAA 330 +RIA RR A ++GAWVREAAVAHA KQ + AA Sbjct: 297 DRIAARRKAWEDGAWVREAAVAHAEKQAVRDKAA 330 Lambda K H 0.318 0.131 0.402 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: 432 Number of extensions: 14 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: 330 Length of database: 331 Length adjustment: 28 Effective length of query: 302 Effective length of database: 303 Effective search space: 91506 Effective search space used: 91506 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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