Align phenylacetyl-CoA 1,2-epoxidase (EC 1.14.13.149) (characterized)
to candidate WP_058857309.1 AS188_RS01200 phenylacetate-CoA oxygenase subunit PaaC
Query= BRENDA::P76079 (248 letters) >NCBI__GCF_001482365.1:WP_058857309.1 Length = 275 Score = 200 bits (509), Expect = 2e-56 Identities = 115/242 (47%), Positives = 150/242 (61%), Gaps = 3/242 (1%) Query: 7 YTLRLGDNCLVLSQRLGEWCGHAPELEIDLALANIGLDLLGQARNFLSYAAELAGEGDED 66 Y L LGD+ L+L+QRLG W APELE D+ALANI LDLLG AR FL+YA G+ ED Sbjct: 37 YALWLGDDALMLAQRLGWWIARAPELEEDIALANIALDLLGHARFFLTYAGTAWGK-TED 95 Query: 67 TLAFTRDERQFSNLLLVEQPNGNFADTIARQYFIDAWHVALFTRLMESRDPQLAAISAKA 126 LA+ RDE +F + LVEQ NG+F TIARQ + L+ RL++S D LAAI+ KA Sbjct: 96 DLAYFRDEEEFRSCRLVEQENGDFGQTIARQLIFSYYQYELYRRLVDSSDATLAAIADKA 155 Query: 127 IKEARYHLRFSRGWLERLGNGTDVSGQKMQQAINKLWRFTAELFDADEIDIALSEEGIAV 186 +KE +YH + W+ RLG GT+ S +++Q ++ +W + ELF DE+ AL EGIAV Sbjct: 156 LKEVQYHQDHASQWILRLGLGTEESKRRVQDGLDYMWPYVDELFHDDELIDAL--EGIAV 213 Query: 187 DPRTLRAAWEAEVFAGINEATLNVPQEQAYRTGGKKGLHTEHLGPMLAEMQYLQRVLPGQ 246 P TLRA ++ + + EA L VP G + G +E G +LAEMQ L R PG Sbjct: 214 RPSTLRADFDRRIAEILGEAGLEVPGIPGAWGGDRSGEFSEQRGHILAEMQVLARQHPGA 273 Query: 247 QW 248 W Sbjct: 274 TW 275 Lambda K H 0.320 0.135 0.405 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: 218 Number of extensions: 8 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: 248 Length of database: 275 Length adjustment: 25 Effective length of query: 223 Effective length of database: 250 Effective search space: 55750 Effective search space used: 55750 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: 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