Table 1. Representation of different replication initiation protein families in the WWTP CCSD metagenomes.
| Pfam | Name | Known repliconsa | Known hostsa |
Abundance % (total)b |
|
|---|---|---|---|---|---|
| Morges | Visp | ||||
| PF04796 | RepA_C | pCAR3, pIPO2T (IncP9), pXAC33, pAP12875, pNL1 | Proteobacteria, Actinobacteria | 45.4 (769) | 2.0 (205) |
| PF01051 | Rep_3 | pRC18, pCL300, pSCFS1, R46 (IncN) | Gamma-, Betaproteobacteria, Firmicutes | 15.7 (266) | 16.2 (1167) |
| PF10134 | RPA | pSD20, pMTH1, pHLHK8 | Mostly Alphaproteobacteria | 7.8 (133) | 69.5 (7145) |
| PF01446 | Rep_1 | pGI1 (RCR group III), pAE78, pLNU5, pLTK2 | Mostly Firmicutes | 6.8 (116) | 6.3 (648) |
| PF08707 | PriCT_2 | pUH24 | Diverse | 6.4 (109) | 2.1 (216) |
| PF07042 | TrfA | pB4, pJP4 (IncP1b), pUO1, R751, pIJB1 | Mostly Proteobacteria | 6.4 (109) | 0.8 (80) |
| PF08708 | PriCT_1 | pLIM (ColE2), pRE25, pEI1, pMG1 | Firmicutes, Proteobacteria, Actinobacteria | 3.7 (62) | 0.9 (97) |
| PF03090 | Replicase | pNC500, pAP2, pA501, pLO2 | Firmicutes, Proteobacteria, Actinobacteria | 2.7 (46) | 0.5 (55) |
| PF09250 | Prim-Pol | pHEN7, pDL10, pCG2 (pBL1 fam) | Firmicutes, Proteobacteria, Actinobacteria | 2.7 (45) | 0.3 (29) |
| PF05144 | Phage_CRI | pNAD1, pVT1, pMM1 | Mostly Gamma- and Betaproteobacteria | 0.8 (14) | 0.0 (2) |
| PF02486 | Rep_trans | pBMB2062, pRE25, pSTK1, pMLU1, pC223 | Firmicutes, Proteobacteria, Actinobacteria | 0.6 (11) | 0.2 (18) |
| PF05732 | RepL | pSMQ1, pKH12, pSN2 | Mostly Firmicutes | 0.6 (11) | 0.3 (29) |
| PF03428 | RP-C | pHCG3, Ti | Mostly Alphaproteobacteria | 0.2 (4) | 0.9 (94) |
| 100 (1695) | 100 (10258) | ||||
Abbreviation: Pfam, protein family.
a
Non-exhaustive list of example plasmid replicons occurring in the ACLAME database. For a full list, see Supplementary Information-File 1.
b
Pfam counts (in parentheses) are the estimated number of gene copies from integrated contig coverage data.