Table 1.
Overrepresented gene families in the genomic neighborhoods of the Pgl defense system
| Gene family | Overrepresented in PDI | No. of genes in pglZ neighborhoods | Comment |
|---|---|---|---|
| COG1002 | Yesa | 52 | Methylase subunit associated with RM systems; often encoded in a separate locus |
| COG4930 | Yes | 42 | ATP-dependent Lon-type protease |
| pfam08747 | Yes | 22 | Uncharacterized protein |
| COG0553 | Yes | 17 | Superfamily II DNA helicase; often fused to a methylase domain |
| pfam08849 | Yes | 15 | Similar to another, uncharacterized, family (DUF3387) which is fused to RM (e.g., GI code 209527353); structure is solved; PDB code 3BHW; mostly alpha-helical protein; DALI reveals structural similarity with recognition domains of RM systems (Z score, >5.3) |
| COG1201 | No | 13 | Lhr-like helicase |
| pfam10923 | No | 13 | ATPase domain-containing protein |
| COG0863 | Yesa | 11 | DNA modification methylase |
| COG1479/COG3472 | Yes | 8 | RloF-like component of potential RM system found in predicted operon for type I RM system (59); contains uncharacterized N-terminal DGQHR domain and C-terminal HNH-type nuclease domain |
| COG1061 | Yesa | 7 | Superfamily II DNA helicase |
| COG2865 | Yes | 7 | Transcriptional regulator containing an HTH domain and diverged ATP-binding domain (Schlafen-like) |
| xls004407 | No | 7 | Homolog of pfam08849 (see above) |
| COG0515 | No | 11 | Duplicated serine/threonine protein kinase domains; some contain nuclease-related NERD domain (26); for C-terminal region, HHPred identifies similarity with RNA polymerase, alpha chain C-terminal domain (probability of 98% for Mflv_3204), and sigma subunit domain (probability of 93%) |
a
Family was in the positive set.