Genome Property Definition Page

Accession	GenProp0831
Name	archaeal core gene set, exactly 1 per genome
Type	GUILD
Description	archaeal 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 Property	GenProp0067: quantitative content

Components

Step Name	Step Num	Required	Evidence (Method)
Peptidyl-tRNA hydrolase PTH2	PTH2	YES	TIGR00283 (HMM): peptidyl-tRNA hydrolase
arCOG00078 fibrillarin-like rRNA methylase	aC00078	YES	PF01269 (HMM): fibrillarin
arCOG00187 metal-binding-domain/4Fe-4S-binding-domain containing ABC transporter, ATP-binding protein	aC00187	YES	TIGR03679 (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 protein	aC00543	YES	TIGR03675 (HMM): arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein
arCOG00985 PUA-domain protein	aC00985	YES	TIGR03684 (HMM): arCOG04150 universal archaeal PUA-domain protein
arCOG01695/DUF814	aC01695	YES	PF05670 (HMM): PF05670 domain
arCOG01863 helix-turn-helix domain protein	aC01863	YES	TIGR00270 (HMM): TIGR00270 family protein
arCOG04112 diphthamide biosynthesis domain protein	aC04112	YES	TIGR03682 (HMM): diphthamide biosynthesis enzyme Dph2
arCOG04150 KH-domain protein	aC04150	YES	TIGR03665 (HMM): arCOG04150 universal archaeal KH domain protein
arCOG04187	aC04187	YES	TIGR00291 (HMM): rRNA metabolism protein, SBDS family
translation elongation factor aEF-2	aEF-2	YES	TIGR00490 (HMM): translation elongation factor aEF-2
translation initiation factor aIF-2	aIF-2	YES	TIGR00491 (HMM): translation initiation factor aIF-2
translation initiation factor aIF-2, alpha subunit	aIF-2a	YES	PF07541 (HMM): eukaryotic translation initiation factor 2 alpha subunit
peptide release factor 1	aRF1	YES	TIGR03676 (HMM): peptide chain release factor 1, archaeal and eukaryotic forms
archaeal ribosomal protein L10P	a_L10	YES	PF00466 (HMM): ribosomal protein uL10
archaeal ribosomal protein L10e	a_L10e	YES	PF00252 (HMM): ribosomal protein L16
archaeal ribosomal protein L12P	a_L12P	YES	TIGR03685 (HMM): 50S ribosomal protein P1
archaeal ribosomal protein L13P	a_L13P	YES	TIGR01077 (HMM): ribosomal protein uL13
archaeal ribosomal protein L14P	a_L14P	YES	TIGR03673 (HMM): 50S ribosomal protein uL14
archaeal ribosomal protein L15P	a_L15P	YES	PF00827 (HMM): ribosomal L15
archaeal ribosomal protein L19e	a_L19e	YES	PF01280 (HMM): ribosomal protein L19e
archaeal ribosomal protein L21e	a_L21e	YES	PF01157 (HMM): ribosomal protein L21e
archaeal ribosomal protein L22P	a_L22	YES	TIGR01038 (HMM): ribosomal protein uL22
archaeal ribosomal protein L24P	a_L24	YES	TIGR01080 (HMM): ribosomal protein uL24
archaeal ribosomal protein L26e	a_L26e	YES	TIGR00405 (HMM): transcription elongation factor Spt5
archaeal ribosomal protein L29	a_L29	YES	TIGR00012 (HMM): ribosomal protein uL29
archaeal ribosomal protein L3P	a_L3	YES	TIGR03626 (HMM): ribosomal protein uL3
archaeal ribosomal protein L30P	a_L30P	YES	TIGR01309 (HMM): ribosomal protein uL30
archaeal ribosomal protein L32	a_L32	YES	PF01655 (HMM): ribosomal protein L32
archaeal ribosomal protein L6P	a_L6P	YES	TIGR03653 (HMM): ribosomal protein uL6
archaeal ribosomal protein L7AE	a_L7AE	YES	TIGR03677 (HMM): ribosomal protein eL8
archaeal ribosomal protein S10P	a_S10P	YES	TIGR01046 (HMM): ribosomal protein uS10
archaeal ribosomal protein S11P	a_S11P	YES	TIGR03628 (HMM): ribosomal protein uS11
archaeal ribosomal protein S12P	a_S12	YES	TIGR00982 (HMM): ribosomal protein uS12
archaeal ribosomal protein S13P	a_S13P	YES	TIGR03629 (HMM): ribosomal protein uS13
archaeal ribosomal protein S17P	a_S17P	YES	TIGR03630 (HMM): ribosomal protein uS17
archaeal ribosomal protein S19P	a_S19P	YES	TIGR01025 (HMM): ribosomal protein uS19
archaeal ribosomal protein S19e	a_S19e	YES	PF01090 (HMM): ribosomal protein S19e
archaeal ribosomal protein S2	a_S2	YES	TIGR01012 (HMM): ribosomal protein uS2
archaeal ribosomal protein S27	a_S27	YES	PF01667 (HMM): ribosomal protein S27
archaeal ribosomal protein S28e	a_S28e	YES	PF01200 (HMM): ribosomal protein S28e
archaeal ribosomal protein S3Ae	a_S3Ae	YES	PF01015 (HMM): ribosomal S3Ae family
archaeal ribosomal protein S3P	a_S3P	YES	TIGR01008 (HMM): ribosomal protein uS3
archaeal ribosomal protein S4P	a_S4P	YES	TIGR01018 (HMM): ribosomal protein uS4
archaeal ribosomal protein S3e	a_S4e	YES	PF00900 (HMM): ribosomal family S4e
archaeal ribosomal protein S5P	a_S5P	YES	TIGR01020 (HMM): ribosomal protein uS5
archaeal ribosomal protein S6e	a_S6e	YES	PF01092 (HMM): ribosomal protein S6e
rchaeal ribosomal protein S7	a_S7	YES	TIGR01028 (HMM): ribosomal protein uS7
archaeal ribosomal protein S8	a_S8	YES	PF00410 (HMM): ribosomal protein uS8
archaeal ribosomal protein S8e	a_S8e	YES	TIGR00307 (HMM): ribosomal protein eS8
archaeal ribosomal protein S9P	a_S9P	YES	TIGR03627 (HMM): ribosomal protein uS9
tRNA nucleotidyltransferase (CCA-adding enzyme)	a_cca	YES	TIGR03671 (HMM): CCA-adding enzyme
archaeal DNA-directed RNA polymerase subunit B	a_rpoB	YES	TIGR03670 (HMM): DNA-directed RNA polymerase subunit B
alanyl-tRNA synthetase	alaS	YES	TIGR03683 (HMM): alanine--tRNA ligase
diphthine synthase	dph5	YES	TIGR00522 (HMM): diphthine synthase
translation initiation factor eIF-5A	eIF-5A	YES	TIGR00037 (HMM): translation elongation factor IF5A
translation initiation factor 2 subunit gamma	eif2g	YES	TIGR03680 (HMM): translation initiation factor 2, gamma subunit
flap structure-specific endonuclease	fen	YES	TIGR03674 (HMM): flap structure-specific endonuclease
glutamyl-tRNA(Gln) amidotransferase, subunit D	gatD	YES	TIGR02153 (HMM): glutamyl-tRNA(Gln) amidotransferase, subunit D
glutamyl-tRNA(Gln) amidotransferase, subunit E	gatE	YES	TIGR00134 (HMM): glutamyl-tRNA(Gln) amidotransferase, subunit E
glutamyl-tRNA synthetase	gltX	YES	TIGR00463 (HMM): glutamate--tRNA ligase
phenylalanyl-tRNA synthetase	pheS	YES	TIGR00468 (HMM): phenylalanine--tRNA ligase, alpha subunit
prolyl-tRNA synthetase	proS	YES	TIGR00408 (HMM): proline--tRNA ligase
proteasome endopeptidase complex, archaeal, alpha subunit	psmA	YES	TIGR03633 (HMM): proteasome endopeptidase complex, archaeal, alpha subunit
DNA repair and recombination protein RadA, archaeal form	radA	YES	TIGR02236 (HMM): DNA repair and recombination protein RadA
DNA-directed RNA polymerase, subunit A'	rpoA1	YES	TIGR02390 (HMM): DNA-directed RNA polymerase subunit A'
DNA-directed RNA polymerase, subunit A''	rpoA2	YES	TIGR02389 (HMM): DNA-directed RNA polymerase, subunit A''
DNA-directed RNA polymerase	rpoE	YES	TIGR00448 (HMM): DNA-directed RNA polymerase
DNA-directed RNA polymerase, subunit N	rpoN	YES	PF01194 (HMM): RNA polymerase, 8 kDa subunit
preprotein translocase, SecY subunit	secY	YES	PF00344 (HMM): preprotein translocase, SecY subunit

Parent Properties

Accession	Name
GenProp0067	quantitative content

Sibling Properties

Accession	Name
GenProp0003	count of DNA molecules
GenProp0004	count of predicted proteins
GenProp0005	count of tRNAs
GenProp0020	HMM hit percentage
GenProp0085	DNA GC content
GenProp0086	DNA size (megabases)
GenProp0108	amino acid abundance (order)
GenProp0122	protein average length
GenProp0134	functional gene clustering - property level
GenProp0152	DNA dinucleotide thermophily metric RR+YY-RY-YR
GenProp0495	sequenced plasmids
GenProp0799	bacterial core gene set, exactly 1 per genome
GenProp0800	bacterial core gene set, 1 or more per genome
GenProp0805	number of ambiguous nucleotide characters
GenProp0815	archaeal-only core gene set
GenProp0832	archaeal core gene set, 1 or more per genome