Align ring 1,2-phenylacetyl-CoA epoxidase PaaC subunit (EC 1.14.13.149) (characterized)
to candidate YP_001312887.1 Smed_4149 phenylacetate-CoA oxygenase subunit PaaI
Query= metacyc::MONOMER-15949 (253 letters) >NCBI__GCF_000017145.1:YP_001312887.1 Length = 261 Score = 271 bits (693), Expect = 1e-77 Identities = 133/247 (53%), Positives = 168/247 (68%), Gaps = 1/247 (0%) Query: 7 LIEYLLRLGDSALIQGQRLCEWCGRAPALEEELALMNVGLDLVGQARNWLDYAAELLADG 66 L E+LL +GD+ L+ G RL EWCG +PALEE++AL N LDL+GQ + WL A E+ G Sbjct: 16 LFEFLLGMGDNTLVLGHRLSEWCGHSPALEEDIALANTALDLIGQTQLWLGLAGEVEGKG 75 Query: 67 RDADHLAFRRDERAYRNLLLVEQPNGDFAVTMAKQFLYDAWHFQVLDGLSRSGDARVAGI 126 R+AD LAF RD R +RNLLL E+PNGD+ T+ +QFL+DAWH+ L GL S D R+A I Sbjct: 76 RNADDLAFLRDVREFRNLLLAERPNGDYGRTLMRQFLFDAWHYLALKGLRASSDPRIAAI 135 Query: 127 AAKALKEVTYHLRRSGEWVQRLGDGTEESHRRMQAAIPQLWRFTVEMSDGDEVEQRLCEA 186 A K KEV YHL RS + V RLGDGT ESH RM+ A+ +LW +T EM + + L A Sbjct: 136 AEKTSKEVAYHLERSRDLVIRLGDGTAESHARMKKALDELWSYTGEMFVNEAHDAALAAA 195 Query: 187 GIAPDPAQIAGAWQAKVAEVFAAATLPLPEPAVNFYLSGRRGLHSEHLGLLLAEMQFLQR 246 G+AP+P + W VAE AATL P+ + G+RGLH+EHLG +LAEMQFLQR Sbjct: 196 GLAPEPESLEAEWNTLVAETLCAATLGKPQGGY-MHRGGKRGLHTEHLGYVLAEMQFLQR 254 Query: 247 AYPDATW 253 AYP A+W Sbjct: 255 AYPGASW 261 Lambda K H 0.321 0.136 0.421 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: 239 Number of extensions: 9 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: 253 Length of database: 261 Length adjustment: 24 Effective length of query: 229 Effective length of database: 237 Effective search space: 54273 Effective search space used: 54273 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 (21.9 bits) S2: 47 (22.7 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