Align ring 1,2-phenylacetyl-CoA epoxidase PaaE subunit (EC 1.14.13.149) (characterized)
to candidate WP_050462981.1 AKL27_RS11605 phenylacetate-CoA oxygenase/reductase subunit PaaK
Query= metacyc::MONOMER-15950 (357 letters) >NCBI__GCF_001189915.1:WP_050462981.1 Length = 357 Score = 408 bits (1049), Expect = e-118 Identities = 193/356 (54%), Positives = 264/356 (74%), Gaps = 1/356 (0%) Query: 1 MSKFHSLTIKEVRPETRDAVSIAFDVPAELADSFRFTQGQHLVMRTQLDGEEVRRSYSIC 60 MSKF+SLT+ V+ ETRD + ++FDVP EL D+F + QGQHL +R+ ++GE++RRSYSIC Sbjct: 1 MSKFYSLTVGNVKKETRDTIVVSFDVPPELKDTFHYQQGQHLTLRSDINGEDLRRSYSIC 60 Query: 61 TGVNDGELRVAIKRVAGGRFSAYANESLKAGQRLEVMPPSGHFHVELDAARHGNYLAVAA 120 + V D +LRVAIKR GG FS +AN++L+ G L+VMPP GHF++ L A +YLA AA Sbjct: 61 SAVQDQQLRVAIKRTPGGAFSTWANDTLQPGLALQVMPPMGHFNMPLAATNEKHYLAFAA 120 Query: 121 GSGITPILSIIKTTLETEPHSRVTLLYGNRSSASTLFREQLEDLKNRYLQRLNLIFLFSR 180 GSGITP+LSIIKTTL+TEP SR TL+YGNR+S++ +F+E+L DLK+ Y++RLNL+++ SR Sbjct: 121 GSGITPMLSIIKTTLQTEPKSRFTLIYGNRASSTVIFKEELTDLKDVYMERLNLVYVMSR 180 Query: 181 EQQDVDLYNGRIDADKCGQLFSRWIDVKALDAAFICGPQAMTETVRDQLKANGMAAERIH 240 EQQD++L+NGRI +KC Q F WI + +DAAFICGP+ M V D L+A+GM I Sbjct: 181 EQQDIELFNGRITREKCDQFFKHWIQLDDVDAAFICGPEDMIHAVSDSLQAHGMNKSDIK 240 Query: 241 FELFAAAGSAQKREARESAAQDSSVSQITVISDGRELSFELPRNSQSILDAGNAQGAELP 300 ELFAA+ K ++TV+ DG F + + +S+LDA G ++ Sbjct: 241 VELFAASIPKNKANVVRPVI-GKQECEVTVVIDGYHTVFTMEKEKESLLDAALKNGIDMR 299 Query: 301 YSCKAGVCSTCKCKVVEGEVEMDSNFALEDYEVAAGYVLSCQTFPISDKVVLDFDQ 356 YSCK GVC+TC+CKVV+G+V+MD N+ALEDYE+A G+VLSCQ+FP++DKV++DFDQ Sbjct: 300 YSCKGGVCATCRCKVVDGKVDMDVNYALEDYEIARGFVLSCQSFPVTDKVLVDFDQ 355 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: 410 Number of extensions: 13 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: 357 Length of database: 357 Length adjustment: 29 Effective length of query: 328 Effective length of database: 328 Effective search space: 107584 Effective search space used: 107584 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 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