Table 6.
Comparison of bacterial list of total proteins in prokaryote interaction signaling pathways and microbiota metagenomic inference over-represented pathways.
| Metabolism of terpenoids and polyketides | ||||
|---|---|---|---|---|
| Protein | Gen | Phylum | Gram | Pathway |
| GALLSTONES | ||||
| ISPE_RHOP5 | ispE | Proteobacteria | Negative | Terpenoid backbone biosynthesis |
| ISPG_HAEIE | ispG | Proteobacteria | Negative | Terpenoid backbone biosynthesis |
| ISPG_SHEON | ispG | Proteobacteria | Negative | Terpenoid backbone biosynthesis |
| MIAA_PSECP | miaA | Actinobacteria | Positive | Zeatin biosynthesis |
| FADJ_PECCP | fadJ | Proteobacteria | Negative | Limonene and pinene degradation Geraniol degradation |
| TKT1_ECOLI | tktA | Proteobacteria | Negative | Biosynthesis of ansamycins |
| CARCINOMA | ||||
| ISPE_RHOFT | ispE | Proteobacteria | Negative | Terpenoid backbone biosynthesis |
| ISPG_GRABC | ispG | Proteobacteria | Negative | Terpenoid backbone biosynthesis |
| SRFAB_BACSU | srfAB | Firmicutes | Positive | Nonribosomal peptide structures |
| Biosynthesis of others secondary metabolites | ||||
| Protein | Gen | Phylum | Gram | Pathway |
| GALLSTONES | ||||
| DAPB_STRAW | dapB | Actinobacteria | Positive | Monobactam biosynthesis |
| CARCINOMA | ||||
| PROA_LEPBL | proA | Spirochaetes | Negative | Carbapenem biosynthesis |
| PROA_ALKOO | proA | Firmicutes | Positive | Carbapenem biosynthesis |
| DAPB_GEOKA | dapB | Firmicutes | Positive | Monobactam biosynthesis |
| DAPB_STRAW | dapB | Actinobacteria | Positive | Monobactam biosynthesis |
| DAPA_RHOFT | dapA | Proteobacteria | Negative | Monobactam biosynthesis |
| PGCA_BACSU | pgcA | Firmicutes | Positive | Streptomycin biosynthesis |
| HIS8_WOLSU | hisC | Proteobacteria | Negative | Novobiocin biosynthesis |
| TRPE_THET8 | trpE | Deinococcus | Negative | Phenazine biosynthesis |
| Cellular Community—Prokaryotes | ||||
| Protein | Gen | Phylum | Gram | Pathway |
| GALLSTONES | ||||
| SECA_LACAC | secA | Firmicutes | Positive | Quorum sensing |
| SECA_CLOTH | secA | Firmicutes | Positive | Quorum sensing |
| YIDC_METCA | yidC | Proteobacteria | Negative | Quorum sensing |
| LUXS_DESPS | luxS | Proteobacteria | Negative | Quorum sensing, biofilm formation |
| CARCINOMA | ||||
| SP0A_CLOBU | spo0A | Firmicutes | Negative | Quorum sensing |
| SECA_CLOTH | secA | Firmicutes | Positive | Quorum sensing |
| SRFAB_BACSU | srfAB | Firmicutes | Positive | Quorum sensing |
| PTGA_SHIFL | crr | Proteobacteria | Negative | Biofilm formation |
| TRPE_THET8 | trpE | Deinococcus | Negative | Biofilm formation |
| CHEB2_BURPS | cheB2 | Proteobacteria | Negative | Biofilm formation |
Source: Kyoto Encyclopedia of Genes and Genomes. Bold indicates Bacterial proteins included in the carcinogenesis model.