Align ring 1,2-phenylacetyl-CoA epoxidase PaaC subunit (EC 1.14.13.149) (characterized)
to candidate RR42_RS23735 RR42_RS23735 phenylacetic acid degradation protein
Query= metacyc::MONOMER-15949 (253 letters) >FitnessBrowser__Cup4G11:RR42_RS23735 Length = 266 Score = 211 bits (538), Expect = 9e-60 Identities = 125/266 (46%), Positives = 156/266 (58%), Gaps = 18/266 (6%) Query: 3 PNHDLIEYLLRLGDSALIQGQRLCEWCGRAPALEEELALMNVGLDLVGQARNWLDYAA-- 60 P H + Y+LRL D+ALI GQR EWC + PALEE++AL N+ LDL+GQAR +AA Sbjct: 4 PQH--LSYVLRLADNALILGQRNSEWCSQGPALEEDIALANISLDLIGQARLLYSHAATL 61 Query: 61 -ELLADGRDA-DHLAFRRDERAYRNLLLVEQPN-----------GDFAVTMAKQFLYDAW 107 E L R D A+ R ER + N LVE P+ D+AVT+ + FLY A Sbjct: 62 DEALNGARKTEDSYAYFRAEREFANYTLVELPHFGPLAGTARAERDYAVTITRNFLYSAL 121 Query: 108 HFQVLDGLSRSGDARVAGIAAKALKEVTYHLRRSGEWVQRLGDGTEESHRRMQAAIPQLW 167 + L S D +A IAAK+LKE YHL + +W+ R GDGTEESHRR QAA+ L Sbjct: 122 MGHLWTALQSSTDTHLAAIAAKSLKETRYHLTHAADWLIRFGDGTEESHRRAQAALDYLM 181 Query: 168 RFTVEMSDGDEVEQRLCEAGIAPDPAQIAGAWQAKVAEVFAAATLPLPEPAVNFYLSGRR 227 +T E D VE + AGI P A + AWQA VA A ATL LP A + +G+ Sbjct: 182 PYTREFFAADAVETAVAAAGIGPLMADLQPAWQADVAATVAQATLTLPSEAKHI-TTGKH 240 Query: 228 GLHSEHLGLLLAEMQFLQRAYPDATW 253 G HSEH+G LL+EMQ L R +P ATW Sbjct: 241 GEHSEHMGYLLSEMQSLARQHPGATW 266 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: 184 Number of extensions: 11 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: 266 Length adjustment: 24 Effective length of query: 229 Effective length of database: 242 Effective search space: 55418 Effective search space used: 55418 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