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Table 1 Genomic context analysis of R.Hpy188I family members

From: Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site

R.Hpy188I family membera

Neighboring MTase homolog

 

GI (REBASE)

Truncationb

GI (REBASE)

Truncationb

Relationship to other proteins (PFAM, TIGRFAMs and BLASTPc)

Nucleotide sequence

R.Hpy188I branch

8248059 (R.Hpy188I)

-

8248058 (M.Hpy188I)

-

Experimental [26]

8248057

8052220 (R.HpyF17I)

-

8052219 (M.HpyF17I)

-

TIGR02986, M.Hpy188I

8052218

137606550 (Marine)

5'

137606551

5'

M.Hpy188I

137606549 (env_nt)

138608358 (Marine)

5'

138608359, 138608360d

5', gap

M.Hpy188I

138608357 (env_nt)

134801317 (Marine)

5'

N.A.e

N.A.

N.A.

134801314 (env_nt)

136020097 (Marine)

3'

136020096

5'

M.EsaSS1928P

136020095 (env_nt)

137734056 (Marine)

5'

N.A.e

N.A.

N.A.

137734055 (env_nt)

139454792 (Marine)

5'

139454794, 139454795d

gap

M.Hpy188I

139454791 (env_nt)

139696470 (Marine)

3'

N.A.e

N.A.

N.A.

139696468 (env_nt)

140559819 (Marine)

5'f and 3'

N.A.e

N.A.

N.A.

140559817 (env_nt)

140872195 (Marine)

3'f

140872191

5'f

M.EsaSS1928P

140872190 (env_nt)

135963558 (Marine)

5'

135963559, 135963560g

complex

M.Hpy188I

135963557 (env_nt)

136192486 (Marine)

5'

136192485, 136192487h

frameshift

PF02384.7, M.Hpy188I

136192484 (env_nt)

R.HpyAORF481P branch

135833547 (Marine)

5'

135833548

3'

PF02086.6, M.HpyAORF481P

135833546 (env_nt)

144033223 (Marine)

3'

144033224

-

M.MunI

144033222 (env_nt)

141400025 (Marine)

3'

141400026

5' and 3'f

PF02086.6, M.HpyAORF481P

141400023 (env_nt)

143652664 (Marine)

-

143652663

-

PF02086.6, M.HpyAORF481P

143652662 (env_nt)

134783906 (Marine)

3'

N.A.e

N.A.

N.A.

134783905 (env_nt)

135316365 (Marine)

5'

N.A.e

N.A.

N.A.

135316364 (env_nt)

144056752 (Marine)

5'

144056751

3'

PF02086.6, M.HpyAORF481P

144056750 (env_nt)

108562884 (R.HpyHORF458P)

-

108562883 (M.HpyHORF458P)

-

PF02086.6, M.HpyAORF481P

108562424i

15611501 (R.Hpy99ORF433P)

-

15611500 (M.Hpy99ORF433P)

-

PF02086.6, M.HpyAORF481P

15611071j

15645110 (R.HpyAORF481P)

-

15645109 (M.HpyAORF481P)

-

PF02086.6, M.HpyAORF481P

15644634k

57242192 (R.CupORF237P)

-

57242195 (M.CupORF237P)

-

PF02086.6, M.HpyAORF481P

57242183l

58533050 (Synpha)

-

58532812 (M.SspSPM2ORFAP)

-

PF02086.6, M.HpyAORF481P

58532811

  1. N.A., Not applicable.
  2. a The order of the sequences is the same as their order in Figure 1.
  3. b End of the cloned DNA fragment or end of the sequenced part of the cloned fragment. 5' or 3' indicate missing sequence data at the 5' or 3' side of the putative nuclease or MTase gene (corresponding to truncation of N- or C- terminus of the protein sequence, respectively).
  4. c A homologous MTase is described by its REBASE name.
  5. d The MTase gene includes an internal gap (unsequenced fragment).
  6. e A MTase gene was not detected on one side of the REase gene, but the other side is not available for analysis, thus the presence of the MTase cannot be either excluded or confirmed.
  7. f The clone contains an internal gap (unsequenced fragment), which overlaps with one end of the gene.
  8. g Probably a combination of rearrangement(s) and frameshift(s)
  9. hA frameshift mutation splits the MTase gene.
  10. i Genomic neighborhood includes also M.HpyHORF460P (GI 108562885).
  11. j Genomic neighborhood includes also R.Hpy99XIP (GI 15611503) and M.Hpy99XI (GI 15611502).
  12. kGenomic neighborhood includes also R.HpyAORF483P (GI 15645111) and M.HpyAORF483P (pseudogene).
  13. l Another putative RM system comprising M.CupORF235P (GI 57242193) and CUP0236 (GI 57242194; not in REBASE; a homolog of HacSORF520P from REBASE) is inserted into the CupORF237P RM system.
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BMC Structural Biology

ISSN: 1472-6807

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