Align 1,2-phenylacetyl-CoA epoxidase, subunit E; 1,2-phenylacetyl-CoA epoxidase, reductase subunit; 1,2-phenylacetyl-CoA monooxygenase, subunit E; EC 1.-.-.- (characterized)
to candidate WP_013093047.1 BC1002_RS26340 NO-inducible flavohemoprotein
Query= SwissProt::P76081 (356 letters) >NCBI__GCF_000092885.1:WP_013093047.1 Length = 393 Score = 91.3 bits (225), Expect = 4e-23 Identities = 70/228 (30%), Positives = 106/228 (46%), Gaps = 10/228 (4%) Query: 18 DAVTITFAVPQPLQEAYRFRPGQHLTLKASFDGEELRRCYSICRSYLPGEISVAVKAIEG 77 D +T + P E F+PGQ++ ++ DGEE+RR YS+ E ++VK Sbjct: 168 DEITSFYLRPDDGGELLAFKPGQYIGVRLVIDGEEVRRNYSLSAMSDGREYRISVKHEPN 227 Query: 78 GRFSRYAREHIRQGMTLEVMVPQGHFGYQPQAERQGRYLAIAAGSGITPMLAIIATTLQT 137 G S Y E +++ TLE+ P G F QP + + I+ G GITP +A++ L+T Sbjct: 228 GTVSTYLHEQMKENDTLELFAPAGEFTLQPGDK---PLVLISGGVGITPTMAMLQAALKT 284 Query: 138 EPESQFTLIYGNRTSQSMMFRQALADLKDKYPQRLQLLCIFSQETLDSDL-LHGRIDGEK 196 F I+ R FR A+ L ++PQ + C + D+D G +D Sbjct: 285 NRPVHF--IHAARHGGVHAFRGAIDALAARHPQLKRFYCYEQRRDGDADAHAVGYVDEAN 342 Query: 197 LQSLGASLINFRLYDEAFICGPAAMMDDAETALKALGMPDKTIHLERF 244 L+ L R D F+ GP A M + LKA+G+P+ E F Sbjct: 343 LKKW---LPETRDVDVYFL-GPIAFMKAIKKCLKAIGVPESQSRYEFF 386 Lambda K H 0.320 0.135 0.390 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: 319 Number of extensions: 12 Number of successful extensions: 2 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: 356 Length of database: 393 Length adjustment: 30 Effective length of query: 326 Effective length of database: 363 Effective search space: 118338 Effective search space used: 118338 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: 50 (23.9 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