Align ring 1,2-phenylacetyl-CoA epoxidase PaaC subunit (EC 1.14.13.149) (characterized)
to candidate BPHYT_RS18260 BPHYT_RS18260 phenylacetic acid degradation protein
Query= metacyc::MONOMER-15949 (253 letters) >FitnessBrowser__BFirm:BPHYT_RS18260 Length = 267 Score = 204 bits (519), Expect = 2e-57 Identities = 115/268 (42%), Positives = 155/268 (57%), Gaps = 18/268 (6%) Query: 1 MNPNHDLIEYLLRLGDSALIQGQRLCEWCGRAPALEEELALMNVGLDLVGQARNWLDYAA 60 + P H ++Y+LRL D+ALI GQR EWCG P LEE++AL N+ LDL+GQAR +AA Sbjct: 3 ITPQH--LQYVLRLADTALILGQRNTEWCGHGPILEEDIALSNMSLDLIGQARLLYTHAA 60 Query: 61 ----ELLADGRDADHLAFRRDERAYRNLLLVEQPN-----------GDFAVTMAKQFLYD 105 +L R D A+ R ER + N L E P+ D+AVT+ + FLY Sbjct: 61 SLEQQLTGKNRTEDDYAYFRAEREFANYTLAELPHVGPLSATAKAEKDYAVTIVRNFLYS 120 Query: 106 AWHFQVLDGLSRSGDARVAGIAAKALKEVTYHLRRSGEWVQRLGDGTEESHRRMQAAIPQ 165 + L+ S D ++A IA+K++KE +YH+ + EW+ R GDGTEESHRR Q A+ Sbjct: 121 TLMAHLWTALTASTDEQLAAIASKSIKETSYHVHHAREWLIRFGDGTEESHRRAQTALDY 180 Query: 166 LWRFTVEMSDGDEVEQRLCEAGIAPDPAQIAGAWQAKVAEVFAAATLPLPEPAVNFYLSG 225 L ++ E D VE+ + AGI P + + AW V ATL LPEP V +G Sbjct: 181 LVPYSREFFSTDAVEESIAAAGIGPLTSDLETAWLDDVRATLDEATLTLPEP-VKHVTTG 239 Query: 226 RRGLHSEHLGLLLAEMQFLQRAYPDATW 253 + G HSEH+G +LAEMQ L R +P ATW Sbjct: 240 KHGEHSEHMGFVLAEMQSLARQHPGATW 267 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: 173 Number of extensions: 7 Number of successful extensions: 3 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: 267 Length adjustment: 24 Effective length of query: 229 Effective length of database: 243 Effective search space: 55647 Effective search space used: 55647 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:
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