Align ring 1,2-phenylacetyl-CoA epoxidase PaaE subunit (EC 1.14.13.149) (characterized)
to candidate BPHYT_RS18270 BPHYT_RS18270 phenylacetic acid degradation protein
Query= metacyc::MONOMER-15950 (357 letters) >FitnessBrowser__BFirm:BPHYT_RS18270 Length = 362 Score = 357 bits (916), Expect = e-103 Identities = 175/358 (48%), Positives = 238/358 (66%), Gaps = 5/358 (1%) Query: 3 KFHSLTIKEVRPETRDAVSIAFDVPAELADSFRFTQGQHLVMRTQLDGEEVRRSYSICTG 62 +FH L I+EVRPET D+VS+AF+VPAEL D +RFTQGQ + ++T +DGEE RRSYSIC G Sbjct: 5 QFHPLRIREVRPETADSVSVAFEVPAELRDHYRFTQGQFVTLKTHIDGEETRRSYSICVG 64 Query: 63 VND----GELRVAIKRVAGGRFSAYANESLKAGQRLEVMPPSGHFHVELDAARHGNYLAV 118 V D GELR+ IKRV GGRFS +A ++L+ G ++VM P G F L+A + YLA Sbjct: 65 VTDYDRDGELRIGIKRVRGGRFSNFAFDTLQPGHTIDVMTPDGRFFTHLNADQGQQYLAF 124 Query: 119 AAGSGITPILSIIKTTLETEPHSRVTLLYGNRSSASTLFREQLEDLKNRYLQRLNLIFLF 178 + GSGITP+L+IIKTTLE EP S TL+YGNRS +F E+LEDLKNR++ R L + Sbjct: 125 SGGSGITPVLAIIKTTLEVEPRSTFTLVYGNRSVDQIMFAEELEDLKNRFMNRFVLYHVL 184 Query: 179 SREQQDVDLYNGRIDADKCGQLFSRWIDVKALDAAFICGPQAMTETVRDQLKANGMAAER 238 S + QDV+L+NG +D DKC + A+D AFICGP M + LKA G+ +E+ Sbjct: 185 SDDLQDVELFNGVLDQDKCAAFIENLLPADAIDEAFICGPAPMMDAAEAALKAAGVPSEK 244 Query: 239 IHFELFAAAGSAQKREARESAAQDSSVSQITVISDGRELSFELPRNSQSILDAGNAQGAE 298 +H E F + Q +D+ + + ++ DG+ LP S+LD G G Sbjct: 245 VHVERFGSP-LPQAGVPPVEITEDTPAADLEIVLDGKRRKLRLPYQGVSVLDVGLRAGLA 303 Query: 299 LPYSCKAGVCSTCKCKVVEGEVEMDSNFALEDYEVAAGYVLSCQTFPISDKVVLDFDQ 356 LPY+CK GVC TC+ KV+EGEV+M+ N+ LE++E+ G+VL+CQ PISD+VV+ +D+ Sbjct: 304 LPYACKGGVCCTCRAKVLEGEVKMEKNYTLEEHEIRDGFVLTCQCHPISDRVVVSYDE 361 Lambda K H 0.319 0.133 0.377 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: 398 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: 357 Length of database: 362 Length adjustment: 29 Effective length of query: 328 Effective length of database: 333 Effective search space: 109224 Effective search space used: 109224 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 (21.8 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