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Table 2 Predictions of H. volcanii rRNA modifications genes

From: RNomics and Modomics in the halophilic archaea Haloferax volcanii: identification of RNA modification genes

Position

Modification

Prediction method

Hv orfa

COG

Commentsb

5S

     

None

None

    

16S C

     

910 (966)

acp3U

Prediction this work

HVO_0390

2016

See text, 1Q7H

1352 (1404)

C* = N330

 

?

?

See text

1432 (1500)

m6A

Prediction this work

HVO_1475

2263

See text, 1QAN

1450+1451 (1518+1519)

m62A

Homology with M. jannaschii RsmA* [137]

HVO_2746

0030

 

23S Data From H. marismortuiD

     

628 (571)

m1A

Prediction, weak homology with E. coli RlmA [146]

HVO_0309

2226

 

1950 (1909)

Gm

aFib+ sRNA

  

See Additional file 8

1956+1958 (1915+1917)

Ψ,Ψ

Cbf5+ sRNA

  

See Additional file 8

2587 (2552)

Um

Homology with E. coli RlmE [138]

HVO_0180

1189

 

2588 (2553)

Gm

Prediction RlmE?

HVO_0180

1189

See text

2619 (2584)

m3U

Prediction, this work and [93]

HVO_2565

2016

See text, 1K3R

2621 (2586)

Ψ

Cbf5+ sRNA

  

See Additional file 8

Guide RNA protein machinery

     

Cbf5

 

Homology P. furiosus Cbf5* [183]

HVO_2493

0103

2AUS, 2RFK, 2APO

Gar1p

 

Homology P. furiosus Gar1p* [183]

HVO_1108

3277

2HVY, 2EY4 2RFK

Nop10

 

Homology P. furiosus Nop10* [183]

HVO_0698

2260

2AUS

L7Ae

 

Homology S. solfataricus L7* [184]

HVO_2737

1358

1PXW, 2FC3, 1RLG, 1SDS, 2QA4

Fibrillarin

 

Homology with S. solfataricus aFib* [184]

HVO_1669

1889

1NT2, 1PRY 1G8S, 1FBN, 1G8A

Nop56/58

 

Homology S. solfataricus Nop56/58* [184]

HVO_1670

1498

1NT2

  1. aRefSeq annotation in archaea.ucsc.edu/;bif the structure of an Archaeal member of the family is available the PDB code is given ; *Experimentally verified; c H. volcanii numbering corresponding E. coli numbering given in brackets; d H. marismortui positions corresponding E. coli position in brackets