tRNA intron endonuclease: The case of the missing tRNA

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My Favorite Pathway DNA Replication
in Halorhabdus utahensis
Peter Bakke
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DNA Replication Comparison

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DNA Replication Comparison

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Visualizing the Origin of Replication
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Cdc6/Orc1
Visualizing the Origin of Replication
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Cdc6/Orc1 DNA Polymerase
Visualizing the Origin of Replication
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Cdc6/Orc1 DNA Polymerase Helicase/
Primase
Visualizing the Origin of Replication
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Cdc6/Orc1 DNA Polymerase Helicase/
Primase Replication Factor
Visualizing the Origin of Replication
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Cdc6/Orc1 DNA Polymerase Helicase/
Primase Replication Factor
Visualizing the Origin of Replication
C
B
A
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1000 Bases Upstream of Cdc6/Orc1 A
TGGTTTTCATCCCCCTTCTTTCAGGTGGAGATTCGCCCGCAGATCCGAGA
TAGCGGCCGAAAACGGCCTGTAGAACCGATATGGCGGATTTCGAGATGGC
GATCTTGGTGCAGTTGAACCACAAGAACCGGTGGGTGAAAGGCTATTAAA
AATTTCGGTTCAGATCGTGCCCAGTCGATGATGATGGATTCGGAGAGGTG
ATCATGTCCGGTGAATCAGTTTGCAGAGGTCCAAGCACCGTCCGGATTGG
AGTGGTCTGGTTTCCGGATTGGAGGGAGCCTGGTTTTACAGGCTTCGATG
CGAATTCCCGGAGCTTGCCCCCGAGACGATCCACACATCTGCATGAAGTC
TGGAGAGGTTTGTCATTGAGTGCTATTGTCAAAGACACCCTCCCCCACCC
CTTCGTTTCGAGTGGAACAGTCCAAACACCCGGGGAGGGGGGTTCAGCAA
CCGGGTAAGGACAATCTAGAAAAGTCGGGTTTTATTAGAGAGTACATATA
ACAGTAACCGTAATGGGAACCAATTCTCTCATTGAATAAATTTAAAGTGT
CTAGTAGATATTAGTACTAGATCTACCTAGAACAAAAGTACTAGTTTCCA
CTAGAGGTTCTGTATGGCACTCTCATCTCCATTGACGATGGTTCTCAGTC
GGTACTAATCGGTGTTAGTTGGTCCTTCCTGAGACGATCCGCTGATATAC
TGTCGAACGGTTTCGGCGATCAGTTTGGCCTCACCCGATGCTTTGCCGTT
CTGCTCTACAGTGTAAGATACCGAATCATCCAATATGCATCACGACTGCA
GTAGAAACGATCCCGTGCATTCCGGAGACTGATAGTCTATTATATACTGG
TCTATACCAGTCTGATGTCATGGTTTCGTTATATCTACCCATCGCCAATA
TCGAATCGCCACCGAGTCGGTCTGCGTGTGGATTTTCGCTCGTTCGGACG
ATCTGTACCGGTCAGCGCATGGTCCACCCGGTGGTTCACGGTGTTCCACT
TGAAACGAAGGGGTGGGGGG
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49 GC Content
TGGTTTTCATCCCCCTTCTTTCAGGTGGAGATTCGCCCGCAGATCCGAGA
TAGCGGCCGAAAACGGCCTGTAGAACCGATATGGCGGATTTCGAGATGGC
GATCTTGGTGCAGTTGAACCACAAGAACCGGTGGGTGAAAGGCTATTAAA
AATTTCGGTTCAGATCGTGCCCAGTCGATGATGATGGATTCGGAGAGGTG
ATCATGTCCGGTGAATCAGTTTGCAGAGGTCCAAGCACCGTCCGGATTGG
AGTGGTCTGGTTTCCGGATTGGAGGGAGCCTGGTTTTACAGGCTTCGATG
CGAATTCCCGGAGCTTGCCCCCGAGACGATCCACACATCTGCATGAAGTC
TGGAGAGGTTTGTCATTGAGTGCTATTGTCAAAGACACCCTCCCCCACCC
CTTCGTTTCGAGTGGAACAGTCCAAACACCCGGGGAGGGGGGTTCAGCAA
CCGGGTAAGGACAATCTAGAAAAGTCGGGTTTTATTAGAGAGTACATATA
ACAGTAACCGTAATGGGAACCAATTCTCTCATTGAATAAATTTAAAGTGT
CTAGTAGATATTAGTACTAGATCTACCTAGAACAAAAGTACTAGTTTCCA
CTAGAGGTTCTGTATGGCACTCTCATCTCCATTGACGATGGTTCTCAGTC
GGTACTAATCGGTGTTAGTTGGTCCTTCCTGAGACGATCCGCTGATATAC
TGTCGAACGGTTTCGGCGATCAGTTTGGCCTCACCCGATGCTTTGCCGTT
CTGCTCTACAGTGTAAGATACCGAATCATCCAATATGCATCACGACTGCA
GTAGAAACGATCCCGTGCATTCCGGAGACTGATAGTCTATTATATACTGG
TCTATACCAGTCTGATGTCATGGTTTCGTTATATCTACCCATCGCCAATA
TCGAATCGCCACCGAGTCGGTCTGCGTGTGGATTTTCGCTCGTTCGGACG
ATCTGTACCGGTCAGCGCATGGTCCACCCGGTGGTTCACGGTGTTCCACT
TGAAACGAAGGGGTGGGGGG
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28-base Inverted Repeat
TGGTTTTCATCCCCCTTCTTTCAGGTGGAGATTCGCCCGCAGATCCGAGA
TAGCGGCCGAAAACGGCCTGTAGAACCGATATGGCGGATTTCGAGATGGC
GATCTTGGTGCAGTTGAACCACAAGAACCGGTGGGTGAAAGGCTATTAAA
AATTTCGGTTCAGATCGTGCCCAGTCGATGATGATGGATTCGGAGAGGTG
ATCATGTCCGGTGAATCAGTTTGCAGAGGTCCAAGCACCGTCCGGATTGG
AGTGGTCTGGTTTCCGGATTGGAGGGAGCCTGGTTTTACAGGCTTCGATG
CGAATTCCCGGAGCTTGCCCCCGAGACGATCCACACATCTGCATGAAGTC
TGGAGAGGTTTGTCATTGAGTGCTATTGTCAAAGACACCCTCCCCCACCC
CTTCGTTTCGAGTGGAACAGTCCAAACACCCGGGGAGGGGGGTTCAGCAA
CCGGGTAAGGACAATCTAGAAAAGTCGGGTTTTATTAGAGAGTACATATA
ACAGTAACCGTAATGGGAACCAATTCTCTCATTGAATAAATTTAAAGTGT
CTAGTAGATATTAGTACTAGATCTACCTAGAACAAAAGTACTAGTTTCCA
CTAGAGGTTCTGTATGGCACTCTCATCTCCATTGACGATGGTTCTCAGTC
GGTACTAATCGGTGTTAGTTGGTCCTTCCTGAGACGATCCGCTGATATAC
TGTCGAACGGTTTCGGCGATCAGTTTGGCCTCACCCGATGCTTTGCCGTT
CTGCTCTACAGTGTAAGATACCGAATCATCCAATATGCATCACGACTGCA
GTAGAAACGATCCCGTGCATTCCGGAGACTGATAGTCTATTATATACTGG
TCTATACCAGTCTGATGTCATGGTTTCGTTATATCTACCCATCGCCAATA
TCGAATCGCCACCGAGTCGGTCTGCGTGTGGATTTTCGCTCGTTCGGACG
ATCTGTACCGGTCAGCGCATGGTCCACCCGGTGGTTCACGGTGTTCCACT
TGAAACGAAGGGGTGGGGGG
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28-base Inverted Repeat
TGGTTTTCATCCCCCTTCTTTCAGGTGGAGATTCGCCCGCAGATCCGAGA
TAGCGGCCGAAAACGGCCTGTAGAACCGATATGGCGGATTTCGAGATGGC
GATCTTGGTGCAGTTGAACCACAAGAACCGGTGGGTGAAAGGCTATTAAA
AATTTCGGTTCAGATCGTGCCCAGTCGATGATGATGGATTCGGAGAGGTG
ATCATGTCCGGTGAATCAGTTTGCAGAGGTCCAAGCACCGTCCGGATTGG
AGTGGTCTGGTTTCCGGATTGGAGGGAGCCTGGTTTTACAGGCTTCGATG
CGAATTCCCGGAGCTTGCCCCCGAGACGATCCACACATCTGCATGAAGTC
TGGAGAGGTTTGTCATTGAGTGCTATTGTCAAAGACACCCTCCCCCACCC
CTTCGTTTCGAGTGGAACAGTCCAAACACCCGGGGAGGGGGGTTCAGCAA
CCGGGTAAGGACAATCTAGAAAAGTCGGGTTTTATTAGAGAGTACATATA
ACAGTAACCGTAATGGGAACCAATTCTCTCATTGAATAAATTTAAAGTGT
CTAGTAGATATTAGTACTAGATCTACCTAGAACAAAAGTACTAGTTTCCA
CTAGAGGTTCTGTATGGCACTCTCATCTCCATTGACGATGGTTCTCAGTC
GGTACTAATCGGTGTTAGTTGGTCCTTCCTGAGACGATCCGCTGATATAC
TGTCGAACGGTTTCGGCGATCAGTTTGGCCTCACCCGATGCTTTGCCGTT
CTGCTCTACAGTGTAAGATACCGAATCATCCAATATGCATCACGACTGCA
GTAGAAACGATCCCGTGCATTCCGGAGACTGATAGTCTATTATATACTGG
TCTATACCAGTCTGATGTCATGGTTTCGTTATATCTACCCATCGCCAATA
TCGAATCGCCACCGAGTCGGTCTGCGTGTGGATTTTCGCTCGTTCGGACG
ATCTGTACCGGTCAGCGCATGGTCCACCCGGTGGTTCACGGTGTTCCACT
TGAAACGAAGGGGTGGGGGG
ORIGIN
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Other Evidence
Opposing Gene Directions
Local Minimum in Cumulative GC Skew
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Cdc6/Orc1 DNA Polymerase Helicase/
Primase Replication Factor
Visualizing the Origin of Replication
Origin
2,327,225
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References

Bell, Archaeal DNA Replication A Robust Model
for Eukaryotes, Geothermal Biology and
Geochemistry in Yellowstone National Park
2005. Berquist, An Archaeal Chromosomal
Autonomously Replicating Sequence Element from an
Extreme Halophile, Halobacterium sp. Strain
NRC-1, Journal of Bacteriology 2003. Duggin,
The Chromosome Replication Machinery of the
Archaeon Sulfolobus solfataricus, Journal of
Biological Chemistry 2006. Grabowski,
Archaeal DNA Replication Eukaryal Proteins in a
Bacterial Context, Annual Review of Microbiology
2003. Lopez, Identification of Putative
Chromosomal Origins of Replication in Archaea,
Molecular Biology 2002. McNair, How to
Determine the Origin of Replication in a Genome,
2008.