Align ring 1,2-phenylacetyl-CoA epoxidase PaaA subunit (EC 1.14.13.149) (characterized)
to candidate SM_b21640 SM_b21640 phenylacetate-CoA oxygenase subunit PaaA
Query= metacyc::MONOMER-15947 (330 letters) >FitnessBrowser__Smeli:SM_b21640 Length = 332 Score = 496 bits (1277), Expect = e-145 Identities = 234/322 (72%), Positives = 273/322 (84%), Gaps = 1/322 (0%) Query: 1 MYAQLVETGVKRVKALEEMAPEERAFQERIDAEIKIEAKNWMPDAYRQTLIRQISQHAHS 60 MYAQ+V+T RVK+ ++M P+ERAFQERIDA KIE K WMP+ YR+TLIRQISQHAHS Sbjct: 1 MYAQMVKTDAPRVKSPDDMDPQERAFQERIDAGQKIEPKEWMPEGYRKTLIRQISQHAHS 60 Query: 61 EIVGMLPEGNWVTRAPTLKRKLQLMAKIQDEAGHGLYLYSAMETLGADRDEEIAKLHSGK 120 EIVG LPEGNW+TRAPTL+RK L+AK+QDEAGHGLYLY A ETLG RD +LH+GK Sbjct: 61 EIVGQLPEGNWITRAPTLERKAILLAKVQDEAGHGLYLYCAAETLGVSRDALYEQLHTGK 120 Query: 121 AKYSSIFNYPTLNWADMGAVGWLVDGAAIVNQVVLQRTSYGPYSRAMIRICKEESFHQRQ 180 AKYSSIFNYPTL+WAD+GA+GWLVDGAAI+NQV LQR SYGPYSRAMIRICKEESFHQRQ Sbjct: 121 AKYSSIFNYPTLSWADIGAIGWLVDGAAIMNQVPLQRCSYGPYSRAMIRICKEESFHQRQ 180 Query: 181 GYEILLTMMRHGTQAQKDMVQDAINRLWWPALMMFGPSDEHSPNSAQSMAWKIKRQSNDE 240 GY+IL+ MM+ GT Q+ MVQDA+NR WWP+LMMFGPSD+ S +SAQSMAWKIK+ SNDE Sbjct: 181 GYDILIKMMK-GTPDQRAMVQDALNRWWWPSLMMFGPSDDASVHSAQSMAWKIKQNSNDE 239 Query: 241 LRQRFIDQTVPQLELLGCTAPDPELKWNEERGHYDFGAIDWSEFYEVLKGNGPCNAERIA 300 LRQ+F++QTVPQ E LG T PDP+LKWNEE+G YDFG DW+EF+EV+ GNGPCNAER+ Sbjct: 240 LRQKFVNQTVPQAEYLGLTVPDPDLKWNEEKGGYDFGEPDWNEFFEVIAGNGPCNAERLG 299 Query: 301 TRRNAIDNGAWVREAAVAHARK 322 RR A ++GAW R+ AHA K Sbjct: 300 ARRKAWEDGAWFRDGLTAHAEK 321 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: 468 Number of extensions: 14 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: 330 Length of database: 332 Length adjustment: 28 Effective length of query: 302 Effective length of database: 304 Effective search space: 91808 Effective search space used: 91808 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 17 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