Uropathogenic Escherichia coli (UPEC) are a major cause of urinary tract and bloodstream infections, and possess an array of virulence factors for colonization, survival and persistence. One such factor is the polysaccharide K capsule. Among the different K capsule types, the K1 serotype is strongly associated with UPEC infection. In this study, we sequenced the genome of the K1 UPEC urosepsis strain PA45B, and employed a novel combination of a lytic K1 capsule-specific phage, saturated Tn5 transposon mutagenesis, and high-throughput transposon directed insertion-site sequencing (TraDIS) to identify the complement of genes required for capsule production. Our analysis identified known genes involved in capsule biosynthesis, as well as two additional regulatory genes (mprA and lrhA) that we characterized at the molecular level. Mutation of mprA resulted in protection against K1 phage-mediated killing, a phenotype restored by complementation. We also identified a significantly increased Tn5 insertion frequency upstream of the lrhA gene, and showed that strong expression of LrhA led to loss of capsule production. Further analysis revealed mutation of mprA or overexpression of LrhA resulted in decreased transcription of capsule biosynthesis genes in PA45B, and increased sensitivity to killing in whole blood. Similar phenotypes were also observed in other UPEC strains UTI89 (K1) and CFT073 (K2) when mprA was mutated or LrhA was overexpressed, demonstrating that the effects were neither strain nor capsule type specific. Overall, this study defined the genome of a UPEC urosepsis isolate, and identified and characterized two new regulatory factors that affect UPEC capsule production.