Summary: Replication protein
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Replication proteins (rep) are involved in plasmid replication. The Rep protein binds to the plasmid DNA and nicks it at the double strand origin (dso) of replication. The 3'-hydroxyl end created is extended by the host DNA replicase, and the 5' end is displaced during synthesis. At the end of one replication round, Rep introduces a second single stranded break at the dso and ligates the ssDNA extremities generating one double-stranded plasmid and one circular ssDNA form. Complementary strand synthesis of the circular ssDNA is usually initiated at the single-stranded origin by the host RNA polymerase .
Marsin S, Forterre P; , Mol Microbiol 1998;27:1183-1192.: A rolling circle replication initiator protein with a nucleotidyl-transferase activity encoded by the plasmid pGT5 from the hyperthermophilic archaeon Pyrococcus abyssi. PUBMED:9570403 EPMC:9570403
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000989Replication proteins (rep) are involved in plasmid replication. The Rep protein binds to the plasmid DNA and nicks it at the double strand origin (dso) of replication. The 3'-hydroxyl end created is extended by the host DNA replicase, and the 5' end is displaced during synthesis. At the end of one replication round, Rep introduces a second single stranded break at the dso and ligates the ssDNA extremities generating one double-stranded plasmid and one circular ssDNA form. Complementary strand synthesis of the circular ssDNA is usually initiated at the single-stranded origin by the host RNA polymerase [PUBMED:9570403].
|Cellular component||extrachromosomal circular DNA (GO:0005727)|
|Molecular function||DNA binding (GO:0003677)|
|Biological process||DNA replication (GO:0006260)|
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This clan includes replication proteins for viruses and plasmids. This domain is known to bind DNA. The members of this clan have three motifs. The central HXH is conserved in most families in the clan.
The clan contains the following 9 members:DUF1424 Gemini_AL1 Mob_Pre MobA_MobL Phage_GPA Relaxase Rep_1 T_Ag_DNA_bind Viral_Rep
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Curation and family details
|Seed source:||Prodom_1565 (release 99.1)|
|Number in seed:||25|
|Number in full:||775|
|Average length of the domain:||156.80 aa|
|Average identity of full alignment:||31 %|
|Average coverage of the sequence by the domain:||69.80 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||12|
|Download:||download the raw HMM for this family|
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