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_090440011.1 BLS63_RS03815 ferredoxin:oxidoreductase FAD/NAD(P)-binding protein
Query= SwissProt::P76081 (356 letters) >NCBI__GCF_900100495.1:WP_090440011.1 Length = 516 Score = 190 bits (483), Expect = 6e-53 Identities = 125/350 (35%), Positives = 183/350 (52%), Gaps = 22/350 (6%) Query: 4 FHSLTVAKVESETRDAVTITFAVPQPLQEAYRFRPGQHLTLKASFDGEELRRCYSICRSY 63 F L V + E+ DA + T VP LQE + RPGQ LTLK L RCYS+ + Sbjct: 186 FAGLEVGGRQVESADACSFTLRVPADLQERFAARPGQFLTLKVPCAEPPLLRCYSLSQLP 245 Query: 64 LPGE-ISVAVKAIEGGRFSRYAREHIRQGMTLEVMVPQGHFGYQPQAERQGRYLAIAAGS 122 GE + + VK + GGR S + +H++ G +EV+ P G F + G L + AGS Sbjct: 246 QVGEPLRITVKRVAGGRASNWLFDHLQPGDHIEVLPPAGVF---VPRDLTGDLLLLGAGS 302 Query: 123 GITPMLAIIATTLQTEPESQFTLIYGNRTSQSMMFRQALADLKDKYPQRLQLLCIF--SQ 180 GITP++AI+ L + + + L Y NR + S++F L L+ +YPQRLQL F SQ Sbjct: 303 GITPLMAILQAAL-AQGQGRVCLFYANRDAGSVIFADELKGLQRRYPQRLQLRYWFDASQ 361 Query: 181 ETLDSDLLHGRIDGEKLQSLGASLINFRLYDEAFICGPAAMMDDAETALKALGMPDKTIH 240 ++D + G I + E FICGP MD A AL LG+ ++ I Sbjct: 362 GVPEADAIAGEIADWREA-------------ECFICGPQPFMDGARAALLGLGVIEQRIR 408 Query: 241 LERFNTPGTRVKRSVNVQSDGQKVTVRQDGRDREIVLNADDESILDAALRQGADLPYACK 300 LERF R+ S ++ V +GR E+ + E +L+A + G P AC+ Sbjct: 409 LERFAAQPVSPLRAAKA-SRPSRLRVTLNGRRHELDVQRG-EMLLEAMEQAGLQPPNACR 466 Query: 301 GGVCATCKCKVLRGKVAMETNYSLEPDELAAGYVLSCQALPLTSDVVVDF 350 GVCA CKC+V+ G V M +N +L ++ G+VL+CQA P + ++ V++ Sbjct: 467 SGVCAACKCRVVSGSVTMRSNQALSEQQVRQGWVLACQAEPSSVELQVEY 516 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: 410 Number of extensions: 18 Number of successful extensions: 6 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: 516 Length adjustment: 32 Effective length of query: 324 Effective length of database: 484 Effective search space: 156816 Effective search space used: 156816 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: 51 (24.3 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