DoriC database

DoriC accession number ORI10010002
Organism Helicobacter pylori 26695
RefSeq NC_000915.1
Topology Circular
Lineage Bacteria, Proteobacteria, Epsilonproteobacteria, Campylobacterales, Helicobacteraceae, Helicobacter.
Chromosome size 1667867 nt
Chromosome GC content 0.3887
OriC length 152 nt
OriC AT content 0.6842
The number of DnaA box 3
The location of oriC region 1608998..1609149 nt
The location of dnaA gene 1607624..1608997 nt
The extremes of GC disparity 1635529 nt (minimum), 814087 nt (maximum)
Note Note that the homologous sequence has been confirmed as oriC region using in silico and in vitro studies for the closely-related Helicobacter pylori J99. Please refer to Zawilak A. et al. 2001 (Nucleic Acids Res. 29(11):2251-2259) for more details. Note that the DnaA box motif (tcattcaca) was looked for with no more than one mismatch instead of E. coli perfect DnaA box (ttatccaca).
OriC Sequence

ggcgttattatagcgtgaataagtGGTGAATGAaaaaggaataacaTGTGAATGAaaTGTGAATGAagccttaaaattaaggtgtttcttttaagggtttgtctataatgcttgctttataataagctaatggatgcgaaaaaaggattttc

The information of repeat
The following lines contain repeats found, one line each.
[1] - repeat length of the first part
[2] - starting position of the first part
[4] - repeat length of the second part
[5] - starting position of the second part
[6] - distance of this repeat
[7] - calculated evalue of this repeat
[8] - repeat sequence

For more details, please refer to The Manual of REPuter.

12 19 R 12 19 0 3.87e-04 taagtggtgaat
11 14 R 11 14 0 1.55e-03 gtgaataagtg
11 45 F 11 56 0 1.55e-03 atgtgaatgaa
10 25 F 10 47 0 6.20e-03 gtgaatgaaa
9 25 F 9 58 0 2.48e-02 gtgaatgaa
11 65 P 11 88 -1 5.11e-02 aa[gc]ccttaaaa
8 4 P 8 117 0 9.92e-02 ttattata
8 32 F 8 139 0 9.92e-02 aaaaagga
8 70 R 8 70 0 9.92e-02 ttaaaatt
8 137 R 8 137 0 9.92e-02 gaaaaaag
10 1 R 10 5 -1 1.86e-01 gcg[ta]tattat
10 28 R 10 31 -1 1.86e-01 aa[tg]gaaaaag
7 6 P 7 102 0 3.97e-01 attatag
7 84 R 7 84 0 3.97e-01 tttcttt
9 27 R 9 72 -1 6.69e-01 gaat[gt]aaaa
9 32 R 9 35 -1 6.69e-01 aa[at]aaggaa
9 38 R 9 117 -1 6.69e-01 gaataa[ct]at
9 49 C 9 110 -1 6.69e-01 gaa[tc]gaaat
9 116 P 9 116 -1 6.69e-01 ttat[at]ataa
6 3 P 6 39 0 1.59e+00 gttatt
6 5 C 6 118 0 1.59e+00 tattat
6 14 F 6 25 0 1.59e+00 gtgaat
6 14 F 6 47 0 1.59e+00 gtgaat
6 14 F 6 58 0 1.59e+00 gtgaat
6 16 F 6 38 0 1.59e+00 gaataa
6 16 R 6 120 0 1.59e+00 gaataa
6 17 R 6 38 0 1.59e+00 aataag
6 17 F 6 120 0 1.59e+00 aataag
6 19 R 6 58 0 1.59e+00 taagtg
6 19 R 6 47 0 1.59e+00 taagtg
6 31 F 6 137 0 1.59e+00 gaaaaa
6 31 R 6 139 0 1.59e+00 gaaaaa
6 32 R 6 137 0 1.59e+00 aaaaag
6 43 P 6 43 0 1.59e+00 acatgt
6 68 P 6 76 0 1.59e+00 ccttaa
6 72 C 6 88 0 1.59e+00 aaaatt
6 74 R 6 74 0 1.59e+00 aattaa
6 76 F 6 90 0 1.59e+00 ttaagg
6 87 R 6 146 0 1.59e+00 ctttta
6 103 F 6 117 0 1.59e+00 tataat
6 116 P 6 116 0 1.59e+00 ttataa
6 118 R 6 118 0 1.59e+00 ataata
8 4 F 8 116 -1 2.38e+00 ttat[ta]ata
8 4 C 8 39 -1 2.38e+00 ttatt[ag]ta
8 15 F 8 30 -1 2.38e+00 tgaa[ta]aag
8 16 R 8 30 -1 2.38e+00 gaa[ta]aagt
8 27 C 8 110 -1 2.38e+00 gaa[tc]gaaa
8 28 C 8 84 -1 2.38e+00 aa[ta]gaaaa
8 33 P 8 84 -1 2.38e+00 aaaag[ga]aa
8 36 R 8 139 -1 2.38e+00 aggaa[ta]aa

Refseq NC_000915.1
Legend Figure1 shows the Z-curves for the original sequence. Figure2 shows the Z-curves for the rotated sequence beginning and ending in dif site or the maximum of the GC disparity curve. Short vertical red line indicates the indicator gene (such as dnaA, dnaN, gidA, hemE etc) location, and short up vertical dark blue arrow indicates the identified oriC location, short down vertical brown arrow indicates dif site location. Purple peaks with the diamonds indicates the DnaA box clusters.
Figure 1
zcurve
Figure 2
zcurve

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