A Collection of Clusters that Pose Interesting Puzzles

I am trying to record my observations relating to clusters of genes that tend to occur together in numerous genomes. A number of us consider the clues offered by these clusters to be of overwhelming significance; many other researchers would urge a bit more caution.
I tend to believe that if two or more genes occur close to one another in more than 10 somewhat diverse genomes, then they are somehow functionally linked. Many people, perhaps most, would view this assertion as overstated.
For those who care, here are some puzzles I consider interesting:
  1. A Cluster on the Boundary of Transcription and Translation (or is it Replication?)
  2. PlsX and Related Proteins
  3. DNA Replication: A Cluster Linking a Hypothetical to the ruvABC Genes
  4. A Cluster Containing a Hypothetical Proteins that Appears to be Linked to Replication and Fatty Acid Synthesis
  5. The Relationship Between the Gamma and Tau subunits of DNA Polymerase III and RecR
  6. CoA metabolism: a Little Cluster Worth a Note
  7. Another CoA Cluster Worth Pondering
  8. the "SciH" cluster: Two coupled hypotheticals with no clues
  9. ATP-Dependent DNA Ligase Coupled to a KU-domain Protein
  10. A Hypothetical Coupled to PEP Synthase
  11. A Cluster Relating to Lipopolysaccharide Biosynthesis
  12. A Strange Cluster: No Clues(L25 peptidyl-tRNA hydrolase and RPPK)
  13. A Cluster of Major Importance in the Proteobacter: ndk through engA
  14. A Conserved Cluster in the Gram-Positive Bacteria Containing a Phosphohydrolase and a Phosphate Starvation Induced Gene
  15. An Interesting Cluster Relating to Proline Metabolism: a Risky Conjecture
  16. YicC: the Connections to Ribonuclease PH and Guanylate kinase(?)
  17. A Tough Case
  18. A 3-gene Cluster Containing a cell envelope protein, a protein kinase, and a phosphotransferase