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Table 1 Table of potential Pyl-coding organisms and their pyrrolysine connection

From: Effects of using coding potential, sequence conservation and mRNA structure conservation for predicting pyrrolysine containing genes

Organism

Family

Known Pyl

tRNAPyl

pylS

Whole genome avail

MtxB gene found

Methanosarcina acetivorans

Archaea (Methanosarcinaceae)

Yes

Yes[15]

Yes

Yes

Yes

Methanococcoides burtonii

Archaea (Methanosarcinaceae)

Yes

Yes[15]

Yes

Yes

Yes

Methanosarcina barkeri

Archaea (Methanosarcinaceae)

Yes

Yes[15]

Yes

Yes

Yes

Methanosarcina mazei

Archaea (Methanosarcinaceae)

Yes

Yes[15]

Yes

Yes

Yes

Methanohalophilus mahii

Archaea (Methanosarcinaceae)

Yes

Verified by Infernal

Yes

Yes

Yes

Methanohalobium evestigatum

Archaea (Methanosarcinaceae)

Yes

Verified by Infernal

Yes

Yes

Yes

Methanosarcina thermophila

Archaea (Methanosarcinaceae)

Yes

Verified by Infernal

Yes

No

Yes

Methanosalsum zhilinae

Archaea (Methanosarcinaceae)

Yes

Verified by Infernal

Yes

Yes

Yes

Desulfitobacterium hafniense

Bacteria (Clostridia)

Yes

Yes[15]

Yes

Yes

Yes

Desulfitobacterium autotrophicum

Bacteria (Deltaproteobacteria)

Yes

Yes[15]

Yes

Yes

Yes

Desulfotomaculum acetoxidans

Bacteria( Clostridia)

Yes

Verified by Infernal

Yes

Yes

Yes

Bilophila wadsworthia

Bacteria (Deltaproteobacteria)

Yes

-

Yes

No

Yes

Acetohalobium arabaticum

Bacteria (Clostridia)

Yes

Verified by Infernal

Yes

Yes

Yes

Thermincola potens

Bacteria (Clostridia)

Yes

Verified by Infernal

Yes

Yes

Yes

Desulfosporosinus orientis

Bacteria (Clostridia)

-

Verified by Infernal

Yes

Yes

Yes

Desulfotomaculum gibsoniae

Bacteria (Clostridia)

-

-

Yes

No

Yes

Desulfosporosinus meridiei

Bacteria (Clostridia)

-

-

Yes

No

Yes

Geodermatophilus obscurus

Bacteria (Actinobacteria)

-

Verified by Infernal*

-

No

-

  1. The organisms marked in bold are used in further analyses. We exclude the organisms for which a whole genome sequence is not currently available. We furthermore exclude organisms which do not have both a transfer RNA with UAG anticodon (tRNApyl) and a corresponding tRNA synthetase (pylS).
  2. * No UAG-anticodon.