Align phenylacetyl-CoA 1,2-epoxidase (EC 1.14.13.149) (characterized)
to candidate WP_011764041.1 AZO_RS01550 phenylacetate-CoA oxygenase subunit PaaI
Query= BRENDA::P76079 (248 letters) >NCBI__GCF_000061505.1:WP_011764041.1 Length = 256 Score = 242 bits (617), Expect = 6e-69 Identities = 123/243 (50%), Positives = 159/243 (65%), Gaps = 1/243 (0%) Query: 7 YTLRLGDNCLVLSQRLGEWCGHAPELEIDLALANIGLDLLGQARNFLSYAAELAGEG-DE 65 Y LRL DN L+L QR+ EWCGHAP +E DLAL+N+ LDL+GQAR L++A L G G DE Sbjct: 14 YVLRLADNVLILGQRISEWCGHAPVIEEDLALSNMALDLIGQARLLLTHAGRLEGRGRDE 73 Query: 66 DTLAFTRDERQFSNLLLVEQPNGNFADTIARQYFIDAWHVALFTRLMESRDPQLAAISAK 125 D LAF R ER + NL LVE PN +F T+ R A+ V L+ RL S D +LAAI+AK Sbjct: 74 DQLAFLRVERDYRNLTLVEVPNQDFGRTVVRNMLFGAFQVVLWERLTASADSELAAIAAK 133 Query: 126 AIKEARYHLRFSRGWLERLGNGTDVSGQKMQQAINKLWRFTAELFDADEIDIALSEEGIA 185 ++KEARYH + W+ RLG+GT +S K+Q A+++LW +T E F +DE D A + GI Sbjct: 134 SLKEARYHFSHAAEWVVRLGDGTALSHDKVQAALDELWPYTNEFFASDETDAAAAAAGIG 193 Query: 186 VDPRTLRAAWEAEVFAGINEATLNVPQEQAYRTGGKKGLHTEHLGPMLAEMQYLQRVLPG 245 TL A WE V + +ATL P ++T GK G H+EH+G +LA MQY+QR PG Sbjct: 194 PASNTLEADWENAVLPVLAQATLVAPARTPFKTFGKFGRHSEHMGHLLATMQYMQRTYPG 253 Query: 246 QQW 248 QW Sbjct: 254 AQW 256 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: 165 Number of extensions: 5 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: 248 Length of database: 256 Length adjustment: 24 Effective length of query: 224 Effective length of database: 232 Effective search space: 51968 Effective search space used: 51968 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: 46 (22.3 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