Genome Property Definition Page

Namearchaeal core gene set, exactly 1 per genome
Descriptionarchaeal genome and tend to exhibit little to no lateral gene transfer events. An evaluation of ### publicly available archaeal genomes found greater than 95% having exactly one copy of each of these genes. Models for these genes may also identify genes in eukaryotes or bacteria. The intended use of this property is to evaluate draft Archaeal genomes to determine the degree of completion achieved.
Parent PropertyGenProp0067: quantitative content

Step NameStep NumRequiredEvidence (Method)Evidence Go Terms
Peptidyl-tRNA hydrolase PTH2PTH2YESTIGR00283 (HMM): peptidyl-tRNA hydrolase
arCOG00078 fibrillarin-like rRNA methylaseaC00078YESPF01269 (HMM): fibrillarin
arCOG00187 metal-binding-domain/4Fe-4S-binding-domain containing ABC transporter, ATP-binding proteinaC00187YESTIGR03679 (HMM): arCOG00187 universal archaeal metal-binding-domain/4Fe-4S-binding-domain containing ABC transporter, ATP-binding protein
arCOG00543 universal archaeal KH-domain/beta-lactamase-domain proteinaC00543YESTIGR03675 (HMM): arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein
arCOG00985 PUA-domain proteinaC00985YESTIGR03684 (HMM): arCOG04150 universal archaeal PUA-domain protein
arCOG01695/DUF814aC01695YESPF05670 (HMM): PF05670 domain
arCOG01863 helix-turn-helix domain proteinaC01863YESTIGR00270 (HMM): TIGR00270 family protein
arCOG04112 diphthamide biosynthesis domain proteinaC04112YESTIGR03682 (HMM): diphthamide biosynthesis enzyme Dph2
arCOG04150 KH-domain proteinaC04150YESTIGR03665 (HMM): arCOG04150 universal archaeal KH domain protein
arCOG04187aC04187YESTIGR00291 (HMM): rRNA metabolism protein, SBDS family
translation elongation factor aEF-2aEF-2YESTIGR00490 (HMM): translation elongation factor aEF-2
translation initiation factor aIF-2aIF-2YESTIGR00491 (HMM): translation initiation factor aIF-2
translation initiation factor aIF-2, alpha subunitaIF-2aYESPF07541 (HMM): eukaryotic translation initiation factor 2 alpha subunit
peptide release factor 1aRF1YESTIGR03676 (HMM): peptide chain release factor 1, archaeal and eukaryotic forms
archaeal ribosomal protein L10Pa_L10YESPF00466 (HMM): ribosomal protein uL10
archaeal ribosomal protein L10ea_L10eYESPF00252 (HMM): ribosomal protein L16
archaeal ribosomal protein L12Pa_L12PYESTIGR03685 (HMM): 50S ribosomal protein P1
archaeal ribosomal protein L13Pa_L13PYESTIGR01077 (HMM): ribosomal protein uL13
archaeal ribosomal protein L14Pa_L14PYESTIGR03673 (HMM): 50S ribosomal protein uL14
archaeal ribosomal protein L15Pa_L15PYESPF00827 (HMM): ribosomal L15
archaeal ribosomal protein L19ea_L19eYESPF01280 (HMM): ribosomal protein L19e
archaeal ribosomal protein L21ea_L21eYESPF01157 (HMM): ribosomal protein L21e
archaeal ribosomal protein L22Pa_L22YESTIGR01038 (HMM): ribosomal protein uL22
archaeal ribosomal protein L24Pa_L24YESTIGR01080 (HMM): ribosomal protein uL24
archaeal ribosomal protein L26ea_L26eYESTIGR00405 (HMM): transcription elongation factor Spt5
archaeal ribosomal protein L29a_L29YESTIGR00012 (HMM): ribosomal protein uL29
archaeal ribosomal protein L3Pa_L3YESTIGR03626 (HMM): ribosomal protein uL3
archaeal ribosomal protein L30Pa_L30PYESTIGR01309 (HMM): ribosomal protein uL30
archaeal ribosomal protein L32a_L32YESPF01655 (HMM): ribosomal protein L32
archaeal ribosomal protein L6Pa_L6PYESTIGR03653 (HMM): ribosomal protein uL6
archaeal ribosomal protein L7AEa_L7AEYESTIGR03677 (HMM): ribosomal protein eL8
archaeal ribosomal protein S10Pa_S10PYESTIGR01046 (HMM): ribosomal protein uS10
archaeal ribosomal protein S11Pa_S11PYESTIGR03628 (HMM): ribosomal protein uS11
archaeal ribosomal protein S12Pa_S12YESTIGR00982 (HMM): ribosomal protein uS12
archaeal ribosomal protein S13Pa_S13PYESTIGR03629 (HMM): ribosomal protein uS13
archaeal ribosomal protein S17Pa_S17PYESTIGR03630 (HMM): ribosomal protein uS17
archaeal ribosomal protein S19Pa_S19PYESTIGR01025 (HMM): ribosomal protein uS19
archaeal ribosomal protein S19ea_S19eYESPF01090 (HMM): ribosomal protein S19e
archaeal ribosomal protein S2a_S2YESTIGR01012 (HMM): ribosomal protein uS2
archaeal ribosomal protein S27a_S27YESPF01667 (HMM): ribosomal protein S27
archaeal ribosomal protein S28ea_S28eYESPF01200 (HMM): ribosomal protein S28e
archaeal ribosomal protein S3Aea_S3AeYESPF01015 (HMM): ribosomal S3Ae family
archaeal ribosomal protein S3Pa_S3PYESTIGR01008 (HMM): ribosomal protein uS3
archaeal ribosomal protein S4Pa_S4PYESTIGR01018 (HMM): ribosomal protein uS4
archaeal ribosomal protein S3ea_S4eYESPF00900 (HMM): ribosomal family S4e
archaeal ribosomal protein S5Pa_S5PYESTIGR01020 (HMM): ribosomal protein uS5
archaeal ribosomal protein S6ea_S6eYESPF01092 (HMM): ribosomal protein S6e
rchaeal ribosomal protein S7a_S7YESTIGR01028 (HMM): ribosomal protein uS7
archaeal ribosomal protein S8a_S8YESPF00410 (HMM): ribosomal protein uS8
archaeal ribosomal protein S8ea_S8eYESTIGR00307 (HMM): ribosomal protein eS8
archaeal ribosomal protein S9Pa_S9PYESTIGR03627 (HMM): ribosomal protein uS9
tRNA nucleotidyltransferase (CCA-adding enzyme)a_ccaYESTIGR03671 (HMM): CCA-adding enzyme
archaeal DNA-directed RNA polymerase subunit Ba_rpoBYESTIGR03670 (HMM): DNA-directed RNA polymerase subunit B
alanyl-tRNA synthetasealaSYESTIGR03683 (HMM): alanine--tRNA ligase
diphthine synthasedph5YESTIGR00522 (HMM): diphthine synthase
translation initiation factor eIF-5AeIF-5AYESTIGR00037 (HMM): translation elongation factor IF5A
translation initiation factor 2 subunit gammaeif2gYESTIGR03680 (HMM): translation initiation factor 2, gamma subunit
flap structure-specific endonucleasefenYESTIGR03674 (HMM): flap structure-specific endonuclease
glutamyl-tRNA(Gln) amidotransferase, subunit DgatDYESTIGR02153 (HMM): glutamyl-tRNA(Gln) amidotransferase, subunit D
glutamyl-tRNA(Gln) amidotransferase, subunit EgatEYESTIGR00134 (HMM): glutamyl-tRNA(Gln) amidotransferase, subunit E
glutamyl-tRNA synthetasegltXYESTIGR00463 (HMM): glutamate--tRNA ligase
phenylalanyl-tRNA synthetasepheSYESTIGR00468 (HMM): phenylalanine--tRNA ligase, alpha subunit
prolyl-tRNA synthetaseproSYESTIGR00408 (HMM): proline--tRNA ligase
proteasome endopeptidase complex, archaeal, alpha subunitpsmAYESTIGR03633 (HMM): proteasome endopeptidase complex, archaeal, alpha subunit
DNA repair and recombination protein RadA, archaeal formradAYESTIGR02236 (HMM): DNA repair and recombination protein RadA
DNA-directed RNA polymerase, subunit A'rpoA1YESTIGR02390 (HMM): DNA-directed RNA polymerase subunit A'
DNA-directed RNA polymerase, subunit A''rpoA2YESTIGR02389 (HMM): DNA-directed RNA polymerase, subunit A''
DNA-directed RNA polymeraserpoEYESTIGR00448 (HMM): DNA-directed RNA polymerase
DNA-directed RNA polymerase, subunit NrpoNYESPF01194 (HMM): RNA polymerase, 8 kDa subunit
preprotein translocase, SecY subunitsecYYESPF00344 (HMM): preprotein translocase, SecY subunit

Parent Properties
GenProp0067quantitative content

Sibling Properties
GenProp0003count of DNA molecules
GenProp0004count of predicted proteins
GenProp0005count of tRNAs
GenProp0020HMM hit percentage
GenProp0085DNA GC content
GenProp0086DNA size (megabases)
GenProp0108amino acid abundance (order)
GenProp0122protein average length
GenProp0134functional gene clustering - property level
GenProp0152DNA dinucleotide thermophily metric RR+YY-RY-YR
GenProp0495sequenced plasmids
GenProp0799bacterial core gene set, exactly 1 per genome
GenProp0800bacterial core gene set, 1 or more per genome
GenProp0805number of ambiguous nucleotide characters
GenProp0815archaeal-only core gene set
GenProp0832archaeal core gene set, 1 or more per genome