### Search Overview

Potential PEPC genes identified based on hit to PF00311

Total of 320,503 candidates identified:
IMG isolates (~ bacteria and archaea): 70,597
Phytozome (~ plants): 4,871
IMG metatranscriptomes (~ microbiomes): 3,052
IMG metagenomes (~ microbiomes): 241,621
Phycocosm (~ algae): 280
MycoCosm (~ fungi): 21

These are complete genes with neighboring genes on both ends, and at least 450 amino acids. 

File: PEPC_all.faa - fasta file of all candidate protein sequences

### Non-redundant set of candidates

After redundancy reduction (i.e. removing duplicates), there are 166,405 nonredundant genes:

Phytozome: 2,368
Phycocosm: 253
IMG isolates: 32,733
IMG metagenomes: 130,173
IMG metatranscriptomes: 808
MycoCosm: 21

File: PEPC_unique.faa - fasta file of non-redundant candidate protein sequences

### Potential active sites identification

Active sites were determined based on an alignment to the maize sequence (Phytozome|683|ZmNKH8431.09G093100.1.p)

The maize active-site pattern is RKRRKRRRS. We identified 620 genes with this exact pattern, including 75 genes from high-temperature environments. These genes can be retrieved using:
grep 'HIGH' PEPC_all.ActiveSite.genelist.tsv | grep 'RKRRKRRRS'

Files:
    PEPC_unique.ali: alignment used to identify amino acid at the potential active sites
    PEPC_unique.ActiveSite.genelist.tsv: active site pattern for each non-redundant candidate protein
    PEPC_unqiue.ActiveSite.stat.tsv: aggregated counts of active site patterns (note: most are not identical to the maize version)
    hot_env.tsv: information on the datasets considered as "high temperature" environments