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_027456464.1 K420_RS0101335 phenylacetate-CoA oxygenase/reductase subunit PaaK
Query= SwissProt::P76081 (356 letters) >NCBI__GCF_000519045.1:WP_027456464.1 Length = 365 Score = 305 bits (782), Expect = 9e-88 Identities = 162/364 (44%), Positives = 234/364 (64%), Gaps = 18/364 (4%) Query: 4 FHSLTVAKVESETRDAVTITFAVPQPLQEAYRFRPGQHLTLKASFDGEELRRCYSIC--- 60 FH LT+ +V E +V ITF +P +E + F+PGQ LTL+A +G+++RR YSI Sbjct: 6 FHELTIKRVSPEAAGSVAITFDIPAAARETFDFQPGQFLTLRARVEGQDVRRNYSISSPK 65 Query: 61 -RSYLPGEISVAVKAIEGGRFSRYAREHIRQGMTLEVMVPQGHFGYQ-PQAERQGRYLAI 118 R GE+ + ++ +EGG FS +A + ++ G L+VM P+G F + P+A + + Sbjct: 66 SRLAKAGELEIGIRPVEGGLFSNWAAQTLKAGAKLDVMPPEGRFTIKKPRALHR---VGF 122 Query: 119 AAGSGITPMLAIIATTLQTEPESQFTLIYGNRTSQSMMFRQALADLKDKYPQRLQLLCIF 178 AAGSGITP+L+I ATTL+ +PES+FTL+YGNR S+MF +AL DLKD+YP RL L+ I Sbjct: 123 AAGSGITPILSIAATTLEEQPESKFTLVYGNRRMSSVMFNEALQDLKDRYPDRLTLIHIL 182 Query: 179 SQETLDSDLLHGRIDGEKLQSLGASLINFRLYDEAFICGPAAMMDDAETALKALGMPDKT 238 S++ + DLL GRIDG K+Q++ +L+ DE FICGP AM++ E AL A G+P+ Sbjct: 183 SRQAQEVDLLQGRIDGAKVQAIIDTLLPVASMDEVFICGPEAMIEATERALLAAGVPENR 242 Query: 239 IHLERFNT-PGTRVKRSVNVQSDGQK--------VTVRQDGRDREIVLNADDESILDAAL 289 +H ERF + P K + + K +T+ DG++ E+ + A DE +LDAAL Sbjct: 243 VHTERFTSGPAQAAKIQADTDAAPHKQAAAKDIALTIVLDGKEHELHIGA-DEHVLDAAL 301 Query: 290 RQGADLPYACKGGVCATCKCKVLRGKVAMETNYSLEPDELAAGYVLSCQALPLTSDVVVD 349 G DLP++CK GVC TC+ KVL G+V M+ N++LE DE+ G+VLSCQA T ++ V Sbjct: 302 DAGLDLPFSCKAGVCCTCRAKVLCGEVVMDKNFTLEADEVKQGFVLSCQARATTKNLTVS 361 Query: 350 FDAK 353 FD + Sbjct: 362 FDER 365 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: 346 Number of extensions: 17 Number of successful extensions: 4 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: 365 Length adjustment: 29 Effective length of query: 327 Effective length of database: 336 Effective search space: 109872 Effective search space used: 109872 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