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 YP_002827141.1 NGR_c26310 dioxygenase reductase subunit
Query= SwissProt::P76081 (356 letters) >NCBI__GCF_000018545.1:YP_002827141.1 Length = 368 Score = 132 bits (331), Expect = 2e-35 Identities = 106/345 (30%), Positives = 157/345 (45%), Gaps = 18/345 (5%) Query: 7 LTVAKVESETRDAVTITFAVPQPLQEAYRFRPGQHLTLKASFDGEELRRCYSICRS-YLP 65 L V E D T TFAV + + PGQ +T++ G +L R Y++ S P Sbjct: 28 LVCTSVTDEAPDVKTFTFAVEGG--GWFNYMPGQFITVELRAKGGDLHRTYTVSSSPSRP 85 Query: 66 GEISVAVKAIEGGRFSRYAREHIRQGMTLEVMVPQGHFGYQPQAERQGRYLAIAAGSGIT 125 I++ +KA +R+ E++R G + P GHF + +YL I+AGSGIT Sbjct: 86 YAIAITIKAQPTSIGTRWMFENVRSGSRVRAYGPSGHFTLSRNPGK--KYLFISAGSGIT 143 Query: 126 PMLAIIATTLQTEPESQFTLIYGNRTSQSMMFRQALADLKDKYPQRLQLLCIFSQETLDS 185 PM++++ P+ I R + ++FR+ L L + P L L + ++ S Sbjct: 144 PMMSMLRWLSDCAPDIDVVFINSARRPEEIIFREELELLAKRMPN-LSLGFLPEARSVAS 202 Query: 186 DL--LHGRIDGEKLQSLGASLINFRLYDEAFICGPAAMMDDAETALKALGMPDKTIHLER 243 L GRID KL L + E F CGP M ++A G H E Sbjct: 203 PWAGLMGRIDRHKLSMLTPDFMG----REIFCCGPDPFMRAVSAIVRAEGFDMGHYHQES 258 Query: 244 FNTPG---TRVKRSVNVQSDGQK--VTVRQDGRDREIVLNADDESILDAALRQGADLPYA 298 F T K++ + DG+ VTV G + E V ++IL+ A G +P A Sbjct: 259 FGATSIAETVHKQAREIVLDGKPTGVTVSFLGSNEEQVCEPG-KTILETARAAGVRIPAA 317 Query: 299 CKGGVCATCKCKVLRGKVAMETNYSLEPDELAAGYVLSCQALPLT 343 C+ G+C TCK G+V M N + E+ AGYVL+C + P T Sbjct: 318 CESGICGTCKVLKRSGEVVMHHNGGISDQEINAGYVLACCSRPTT 362 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: 324 Number of extensions: 20 Number of successful extensions: 5 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: 368 Length adjustment: 29 Effective length of query: 327 Effective length of database: 339 Effective search space: 110853 Effective search space used: 110853 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: 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