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*  Sequence Similarity - 1LJO: CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM2) FROM ARCHAEOGLOBUS FULGIDUS AT 1.95A...
Archaeal Sm proteins form heptameric and hexameric complexes: crystal structures of the Sm1 and Sm2 proteins from the ... Archaeal Sm-like protein AF-Sm2 protein, length: 77 (BLAST) Sequence Similarity Cutoff. Rank. Chains in Cluster. Cluster ID / ...
  http://www.rcsb.org/pdb/explore/sequenceCluster.do?structureId=1LJO
*  Stabilization of an archaeal DNA-sliding clamp protein, PCNA, by proteasome-activating nucleotidase gene knockout in Haloferax...
Stabilization of an archaeal DNA-sliding clamp protein, PCNA, by proteasome-activating nucleotidase gene knockout in Haloferax ... Watson JD, Baker TA, Bell SP, Gann A, Levine M & Losick R (2008) Molecular Biology of the Gene. Cold Spring Harbor Laboratory ... Baumann A, Lange C & Soppa J (2007) Transcriptome changes and cAMP oscillations in an archaeal cell cycle. BMC Cell Biol 8: 21 ... Kirkland, P. A. and Maupin-Furlow, J. A. (2009), Stabilization of an archaeal DNA-sliding clamp protein, PCNA, by proteasome- ...
  http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6968.2009.01547.x/references
*  In vitro phosphorylation of initiation factor 2 alpha (aIF2 alpha) from hyperthermophilic archaeon Pyrococcus horikoshii OT3. -...
To examine the properties of archaeal initiation factor 2 alpha (aIF2 alpha), three genes encoding alpha, beta, and gamma ... This finding led us to the search for a putative aIF2 specific kinase gene (PH0512) in the P. horikoshii genome. The gene ... All three subunit genes are conserved in Archaea. ... All three subunit genes are conserved in Archaea. To examine ... This finding led us to the search for a putative aIF2 specific kinase gene (PH0512) in the P. horikoshii genome. The gene ...
  https://www.semanticscholar.org/paper/In-vitro-phosphorylation-of-initiation-factor-2-al-Tahara-Ohsawa/7c9cc114cdfc533491aee79639b0b5950e4dc2e7
*  Evolutionary relationships of bacterial and archaeal glutamine synthetase genes | SpringerLink
Genes for GSI have been found only in bacteria... ... that several lateral gene transfers of archaeal GSI genes to ... In order to study the evolution of GS, we cloned and sequenced GSI genes from two divergent archaeal species: the extreme ... Genes for GSI have been found only in bacteria (eubacteria) and archaea (archaebacteria), while GSII genes only occur in ... Cyanobacterial genes lack adenylylation regulation of GS and may have secondarily lost it. The GSI gene of Sulfolobus ...
  https://link.springer.com/article/10.1007/BF00175876
*  Comparative Analysis of the Methanogen Diversity in Horse and Pony by Using mcrA Gene and Archaeal 16S rRNA Gene Clone Libraries
The archaeal 16S rRNA genes and deduced amino acid sequences of mcrA gene were aligned with Clustal X ver. 2.0 [35], and ... Phylogenetic Analysis of the mcrA Gene and the Archaeal 16S rRNA Gene. No chimeric sequence was found in the present study. A ... Table 5: General information and diversity indices of the mcrA gene and archaeal 16S rRNA gene clone libraries recovered from ... Comparative Analysis of the Methanogen Diversity in Horse and Pony by Using mcrA Gene and Archaeal 16S rRNA Gene Clone ...
  https://www.hindawi.com/journals/archaea/2014/483574/
*  Absynte: a web tool to analyze the evolution of orthologous archaeal and bacterial gene clusters. - PubMed - NCBI
Absynte: a web tool to analyze the evolution of orthologous archaeal and bacterial gene clusters.. Despalins A1, Marsit S, ... Absynte (Archaeal and Bacterial Synteny Explorer) is a web-based service designed to display local syntenies in completely ... Each gene composing the synteny can be further queried interactively using either local or remote databases. Absynte results ... chromosomes from the publicly available archaeal and bacterial genomes. The results consist in a dynamic web page where a ...
  https://www.ncbi.nlm.nih.gov/pubmed/21840875
*  Archaeal integrases and mechanisms of gene capture | Biochemical Society Transactions
... horizontal gene transfer; int, integrase gene; intN and intC, N-terminal and C-terminal part of integrase gene; ORF, open ... Archaeal integrases and mechanisms of gene capture. Q. She, B. Shen, L. Chen ... Archaeal integrases and mechanisms of gene capture Message Subject (Your Name) has forwarded a page to you from Biochemical ... Archaeal integrases facilitate the formation of two distinctive types of integrated element within archaeal chromosomes: the ...
  http://www.biochemsoctrans.org/content/32/2/222
*  MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes | BMC Bioinformatics | Full Text
It continues to be interesting to develop new ab initio algorithms which not only accurately predict genes, but also facilitate ... a lack of comprehensive understanding of prokaryotic gene structures prevents from further elucidation of differences among ... Despite a remarkable success in the computational prediction of genes in Bacteria and Archaea, ... It is still problematic to evaluate gene prediction for archaeal genomes due to the insufficient number of genes confirmed by ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-97
*  Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea | Biology Direct |...
Horizontal Gene TransferGene GainArchaeal GenomeDescendant NodeReverse Gyrase. Background. A robust classification of genes ... The arCOGs were used to reconstruct gene loss and gene gain events during archaeal evolution and gene sets of ancestral forms. ... The Last Archaeal Common Ancestor (LACA) is conservatively estimated to possess 996 genes compared to 1245 and 1335 genes for ... The archaeal gene core (protein-coding genes found in all 41 genome) consists of 166 arCOGs. ...
  https://0-biologydirect-biomedcentral-com.brum.beds.ac.uk/articles/10.1186/1745-6150-2-33
*  When evaluating bacterial and archaeal genomes for genes, why must researchers evaluate six open reading frames? - AnswerMenu
When evaluating bacterial and archaeal genomes for genes, why must researchers evaluate six open reading frames? ... To map genes of a bacterial strain, conjugation must be interrupted at given times. Suppose you have Hfr cells of genotype a+b+ ... For codominant genes, a superscript is used. For example, the human blood type A allele is indicated as 'IA' and the Type B ... For codominant genes, the standard procedure of using capital and lowercase letters for the different alleles is inadequate. ...
  http://www.answermenu.com/3189/evaluating-bacterial-archaeal-researchers-evaluate-reading
*  Gene expression - Conservapedia
What happens to all this excess RNA? Eukaryotic genes (and some Archaeal gene) contain internal 'junk' (discovered in 1977). ... Genes are segments of DNA that contain the information required to make a protein. Gene expression refers to all the processes ... The size of introns is species-specific: yeasts have very few, some human genes can have 50 in a single gene! Typically there ... Gene expression is the process by which a DNA sequence yields a functional product such as, for example, protein.[1] If the DNA ...
  https://www.conservapedia.com/index.php?title=Gene_expression
*  Effects of Rhizophora mangle leaf litter and seedlings on carbon and nitrogen cycling in salt marshes - potential consequences...
1)Archaeal gene for ammonia monooxygenase subunit A, (2) bacterial gene for ammonia monooxygenase subunit A, (3) gene for the ... the bacterial amoA gene, the nxrB gene, the nirK gene, the nirS gene, the norB gene, the nosZ gene, and the nifH gene were 58 ° ... Like the abundance of the archaeal amoA gene, the abundance of the nxrB gene, which is a key gene of nitrite-oxidizing bacteria ... The gene abundances within cluster C1, containing the archaeal amoA, the bacterial amoA, the norB, and the nifH genes, were ...
  https://link.springer.com/article/10.1007%2Fs11104-018-3611-z
*  tbp - TATA-box-binding protein - Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330...
General factor that plays a role in the activation of archaeal genes transcribed by RNA polymerase. Binds specifically to the ... General factor that plays a role in the activation of archaeal genes transcribed by RNA polymerase. Binds specifically to the ... p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source ... Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.,p>,a href='/help/gene_name' target='_top ...
  http://www.uniprot.org/uniprot/O27664
*  tbp - TATA-box-binding protein - Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) - tbp...
General factor that plays a role in the activation of archaeal genes transcribed by RNA polymerase. Binds specifically to the ... General factor that plays a role in the activation of archaeal genes transcribed by RNA polymerase. Binds specifically to the ... p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source ... Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.,p>,a href='/help/gene_name' target='_top ...
  http://www.uniprot.org/uniprot/O58737
*  Antievolution.org - Antievolution.org Discussion Board -Topic::The Origins of Photosynthesis
2000 How Much Did Horizontal Gene Transfer Contribute to Early Evolution?:. Quantifying Archaeal Genes in Two Bacterial ... Gene duplication has generated a heterodimeric reaction center that subsequently evolved to the PSI present in cyanobacteria, ... Further insight into the evolution of photosynthesis will have to rely on additional broader sampling of photosynthesis genes ... Further insight into the evolution of photosynthesis will have to rely on additional broader sampling of photosynthesis genes ...
  http://www.antievolution.org/cgi-bin/ikonboard/ikonboard.cgi?s=59ead8ea899ef7f3
*  Publications
Mehta, M.P., Huber, J.A., and Baross, J.A. (2005). "Incidence of novel and potentially archaeal nitrogenase genes in the deep ... Smith, J., Theodoris, C., and Davidson, E.H. (2007). "A gene regulatory network subcircuit drives a dynamic pattern of gene ... Gribble, K.E., Snell, T.W., and Mark Welch, D.B. (2011). "Gene and protein structure of the mate recognition protein gene ... Gribble, K.E., Snell, T.W., and Mark Welch, D.B. (2010). "Gene and protein structure of the mate recognition protein gene ...
  http://www.mbl.edu/jbpc/publicationsparentpage/
*  Characterization of the First "Candidatus Nitrotoga" Isolate Reveals Metabolic Versatility and Separate Evolution of Widespread...
6 in the main text). The putative nxr genes are shown in orange, and the flanking archaeal genes are shown in blue. Wiggly ... Clustered genes, such as several tRNA genes, may appear as one line owing to space limitations. The tick interval is 0.2 Mbp. ... Genes at loci coding for NXR and hydrogenase, and the predicted functions of the respective gene products, are also shown. NirK ... In addition to the emrE gene on the plasmid (see above), "Ca. Nitrotoga fabula" has another QAC resistance gene (sugE) on the ...
  https://mbio.asm.org/content/9/4/e01186-18
*  TIGR03653
GenProp0815: archaeal-only core gene set (HMM). GenProp0831: archaeal core gene set, exactly 1 per genome (HMM). ... Gene Ontology Term. GO:0003735: structural constituent of ribosome molecular_function. GO:0006412: translation biological_ ... Members of this protein family are the archaeal form ofribosomal protein uL6 (previously L9 in yeast and human). The top- ...
  http://www.jcvi.org/cgi-bin/tigrfams/HmmReportPage.cgi?acc=TIGR03653
*  TIGR01012
Gene Ontology Term. GO:0003735: structural constituent of ribosome molecular_function. GO:0006412: translation biological_ ...
  http://www.jcvi.org/cgi-bin/tigrfams/HmmReportPage.cgi?acc=TIGR01012
*  The archaebacterial origin of eukaryotes | PNAS
2001) Phylogenetic analyses of two "archaeal" genes in Thermotoga maritima reveal multiple transfers between archaea and ... genes (,33). Although many eukaryotic operational genes are thought to have been gained by lateral gene transfer from either ... Gene sequence alignments of small-ribosomal RNA (SSU) genes and large-ribosomal RNA (LSU) genes were manually constructed. The ... Integrative modeling of gene and genome evolution roots the archaeal tree of life ...
  http://www.pnas.org/content/105/51/20356
*  The genetic core of the universal ancestor. - Semantic Scholar
The analysis also identified several genes of unknown function with phylogenies that track with the ribosomal RNA genes. The ... Other universal genes have either undergone lateral transfer in the past, or have diverged so much in sequence that their ... Our analyses identified a small set of genes that can be traced back to the universal ancestor and have coevolved since that ... As indicated by earlier studies, almost all of these genes are involved with the transfer of genetic information, and most of ...
  https://www.semanticscholar.org/paper/The-genetic-core-of-the-universal-ancestor.-Harris-Kelley/152619ece03e2fb89c236cc78723d770cb17fda8
*  Frontiers | Assembly and Succession of Iron Oxide Microbial Mat Communities in Acidic Geothermal Springs | Microbiology
Archaeal and Bacterial 16S rRNA Gene Illumina Sequencing and Analysis. Archaeal and bacterial 16S rRNA gene sequences were ... Barcoded 16S rRNA gene amplification using universal archaeal and bacterial primers (515F/806R; Caporaso et al., 2010; Earth ... For example, populations of a novel archaeal Group 3 (NAG3), which are phylogenetically related to the archaeal order ... 16S rRNA gene sequences (average length = 250 bp) with a database of relevant 16S rRNA gene sequences from YNP hot springs. ...
  https://www.frontiersin.org/articles/10.3389/fmicb.2016.00025/full
*  Frontiers | Dinitrogen fixation in aphotic oxygenated marine environments | Microbiology
Mehta, M. P., Huber, J. A., and Baross, J. A. (2005). Incidence of novel and potentially archaeal nitrogenase genes in the deep ... NifH-like genes were retrieved from the aphotic layer of the LB and were compared with nifH genes from known bacterial isolates ... cyanobacterial nifH genes dominated the photic layer (Langlois et al., 2005); while bacterial nifH genes dominated the deep ... and phylogenetic analysis of the complete nitrogenase structural genes (nifHDK2) and associated genes in the archaeon ...
  https://www.frontiersin.org/articles/10.3389/fmicb.2013.00227/full