Align ring 1,2-phenylacetyl-CoA epoxidase PaaC subunit (EC 1.14.13.149) (characterized)
to candidate 3610439 Dshi_3820 phenylacetate-CoA oxygenase, PaaI subunit (RefSeq)
Query= metacyc::MONOMER-15949 (253 letters) >lcl|FitnessBrowser__Dino:3610439 Dshi_3820 phenylacetate-CoA oxygenase, PaaI subunit (RefSeq) Length = 255 Score = 258 bits (660), Expect = 6e-74 Identities = 133/248 (53%), Positives = 166/248 (66%), Gaps = 2/248 (0%) Query: 7 LIEYLLRLGDSALIQGQRLCEWCGRAPALEEELALMNVGLDLVGQARNWLDYAAELLADG 66 L +L R+GD+ L+ G R+ EWCG AP LEE++AL N LDL+GQ + WL +A + G Sbjct: 9 LFAFLCRMGDNTLVLGHRVSEWCGHAPVLEEDIALANTALDLIGQTQMWLGHAGAVEGKG 68 Query: 67 RDADHLAFRRDERAYRNLLLVEQPNGDFAVTMAKQFLYDAWHFQVLDGLSRSGDARVAGI 126 R AD LA RD +RNLLLVEQPNGDF TM +QFL+DAWH Q+L L+ S + +VA I Sbjct: 69 RSADDLAMLRDVWDFRNLLLVEQPNGDFGQTMMRQFLFDAWHLQMLRALTGSSEPQVAAI 128 Query: 127 AAKALKEVTYHLRRSGEWVQRLGDGTEESHRRMQAAIPQLWRFTVEMSDGDEVEQRLCEA 186 AAK++KEV YHL RSGE V LGDGT ESH RMQAA+ LW + EM D V++ + A Sbjct: 129 AAKSVKEVQYHLERSGEMVIGLGDGTAESHGRMQAALDLLWPYVGEMFQPDPVDRAMAAA 188 Query: 187 GIAPDPAQIAGAWQAKVAEVFAAATLPLPEPAVNFYLSGRRGL-HSEHLGLLLAEMQFLQ 245 GIAPDP+ + + A V V A ATL +PE G+ G HSEHLG +L +MQ+LQ Sbjct: 189 GIAPDPSGLRAGFDAHVDAVLAEATLSIPEGGF-AQTGGKTGFQHSEHLGHMLTQMQWLQ 247 Query: 246 RAYPDATW 253 RAYP A W Sbjct: 248 RAYPGARW 255 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: 221 Number of extensions: 6 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: 255 Length adjustment: 24 Effective length of query: 229 Effective length of database: 231 Effective search space: 52899 Effective search space used: 52899 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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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