Align ring 1,2-phenylacetyl-CoA epoxidase PaaA subunit (EC 1.14.13.149) (characterized)
to candidate WP_089300957.1 CHB84_RS08385 1,2-phenylacetyl-CoA epoxidase subunit A
Query= metacyc::MONOMER-15947 (330 letters) >NCBI__GCF_900188115.1:WP_089300957.1 Length = 324 Score = 461 bits (1187), Expect = e-135 Identities = 215/305 (70%), Positives = 256/305 (83%), Gaps = 1/305 (0%) Query: 23 ERAFQERIDAEIKIEAKNWMPDAYRQTLIRQISQHAHSEIVGMLPEGNWVTRAPTLKRKL 82 ER F++ I + +IE ++WMP+ YR TL+RQI+QHAHSEI+GM PE NW+TRAP+L+RK Sbjct: 12 ERQFEDTIGRDQRIEPRDWMPEGYRSTLVRQIAQHAHSEIIGMQPEANWITRAPSLRRKA 71 Query: 83 QLMAKIQDEAGHGLYLYSAMETLGADRDEEIAKLHSGKAKYSSIFNYPTLNWADMGAVGW 142 L+AK+QDEAGHGLYLYSA ETLGADR E KL SGK KYSSIFNYPTL +AD+G +GW Sbjct: 72 ILLAKVQDEAGHGLYLYSATETLGADRSELTGKLISGKQKYSSIFNYPTLTFADVGVIGW 131 Query: 143 LVDGAAIVNQVVLQRTSYGPYSRAMIRICKEESFHQRQGYEILLTMMRHGTQAQKDMVQD 202 LVDGAAI NQV L R SYGPY+RAMIRICKEESFHQRQGYE+L+TMMR GT Q+ MVQ+ Sbjct: 132 LVDGAAICNQVPLCRCSYGPYARAMIRICKEESFHQRQGYELLMTMMR-GTPGQRRMVQE 190 Query: 203 AINRLWWPALMMFGPSDEHSPNSAQSMAWKIKRQSNDELRQRFIDQTVPQLELLGCTAPD 262 A +R WWP+LMMFGP D SPN+AQSMAWKIKR +NDELRQRF+D TVPQ E LG T PD Sbjct: 191 ATDRWWWPSLMMFGPPDGDSPNTAQSMAWKIKRHTNDELRQRFVDMTVPQAEALGVTLPD 250 Query: 263 PELKWNEERGHYDFGAIDWSEFYEVLKGNGPCNAERIATRRNAIDNGAWVREAAVAHARK 322 P+L+WN ERGHYDFG IDW+EF V+KGNGPCNA+R+A RR+A + G+WVREAA +HA+K Sbjct: 251 PDLRWNAERGHYDFGEIDWTEFTAVVKGNGPCNAQRVAQRRHAHEGGSWVREAAASHAQK 310 Query: 323 QQHKR 327 Q+ +R Sbjct: 311 QEARR 315 Lambda K H 0.318 0.131 0.402 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: 443 Number of extensions: 14 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: 330 Length of database: 324 Length adjustment: 28 Effective length of query: 302 Effective length of database: 296 Effective search space: 89392 Effective search space used: 89392 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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