Table 1.2Non-trivial evolutionary connections and functional predictions for bacteriophage λ proteins

Gene product Evolutionary conservation Structure, Domain architecturea Predicted function, Reference
A (TerL)Bacteriophages, herpesvirusesA modified P-loop ATPase domain, distantly related to a vast class of helicasesATPase subunit of the terminase, involved in DNA packaging in phage head
CBacteria and archaeaClpP protease domainMinor capsid protein, cleaves the scaffold protein during maturation
KBacteria, archaea, and eukaryotesConsists of an N-terminal JAB/MPN domain (predicted metalloprotease) and a C-terminal CHAP domain (Cys,His-dependent DL-glutamate-specific amidohydrolase)Tail subunit; predicted protease involved in tail assembly (based on the presence of the JAB/MPN domain) [679] and peptidoglycan lysis (based on the presence of the peptidoglycan amidohydrolase CHAP domain [948]
Ea31Scattered distribution archaeaEndo VII-colicin domainPredicted nuclease of the McrA (HNH) family [50]
Ea59Bacteria, archaea, and eukaryotesP-loop ATPase domain of the ABC classPredicted ATPase [296]
Exo (RedX)Bacteria, archaea, eukaryotes, virusesλ exonuclease domain, distantly related to a broad variety of nucleasesA nuclease involved in phage recombination and late rolling-circle replication
CIBacteria, archaeaN-terminal helix-turn-helix DNA-binding domain fused to a C-terminal serine protease domain of the LexA/UmuD familyTranscription repressor of genes required for lytic development
CroBacteria, archaeaHelix-turn-helix DNA-binding domainTranscription repressor of early genes
OBacteria, archaeaHelix-turn-helix DNA-binding domainDNA-binding protein involved in the initiation of replication
RenBacteria, archaeaHelix-turn-helix DNA-binding domainProtein involved in exclusion of replication of heterologous genomes in λ-infected bacteria
Nin290Bacteria, archaea, eukaryotesPP-loop ATPase domainPredicted ATP pyrophosphatase, role in phage replication unknown [102]
Nin221Bacteria, archaea, eukaryotesCalcineurin-like serine/threonine protein phosphatase domainProtein phosphatase, role in phage replication unknown [450]

Detailed descriptions of these and other domains are available in the Pfam, SMART, and CDD protein domain databases (see 3.2) and in SCOP and CATH protein structure databases (see 3.3).

From: Chapter 1, Genomics: From Phage to Human

Cover of Sequence - Evolution - Function
Sequence - Evolution - Function: Computational Approaches in Comparative Genomics.
Koonin EV, Galperin MY.
Boston: Kluwer Academic; 2003.
Copyright © 2003, Kluwer Academic.

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