Pyrococcus abyssi
	Annotation DataBase Search Form
	Enter criteria to find out about. Matches are not case sensitive. Click on the submit button after entering your criteria. - Boolean queries are possible with the following operators :'or', 'and', ' not'. Separate these keywords with spaces. - Regular expressions (POSIX 1003.2) are possible with the following operators: '.' (period), '+', '*', '?', '^', '$', '{n}', "|' , '[ ]'. Do NOT separate items with spaces and choose "contains".
	Search in annotation:
	Description Annotation:
	Gene Name:	contains is starts with
	Functional Category:	ALL --------------------- Amino Acid Biosynthesis - Aromatic amino acid family - General - Aspartate family - Glutamate family - Pyruvate family - Serine family - Histidine family --------------------- Purines, Pyrimidines, Nucleosides & Nucleotides - 2'-Deoxyribonucleotide metabolism - Nucleotide and nucleoside interconversions - Purine ribonucleotide biosynthesis - Pyrimidine ribonucleotide biosynthesis - Salvage of nucleosides and nucleotides --------------------- Fatty Acid & Phospholipid Metabolism - Biosynthesis - Degradation - Other --------------------- Cofactors, Prosthetic groups & Carriers Biosynthesis - Heme and porphyrin - Menaquinone and ubiquinone - Molybdopterin - Riboflavin - Thiamine - Pyridine nucleotides - Other --------------------- Central Intermediary Metabolism - Polyamine biosynthesis - Sulfur metabolism - Other --------------------- Autotrophic Metabolism - Photoautotrophy - Chemoautotrophy --------------------- Energy Metabolism - Polysaccharides - Amino acids and amines - Anaerobic - ATP-proton motive force interconversion - Electron transport - Fermentation - Glycolysis/gluconeogenesis - Pentose phosphate pathway - Sugars - TCA cycle --------------------- Transport & Binding Proteins - Amino acids, peptides and amines - Anions - Carbohydrates, organic alcohols, and acids - Cations - Other - Unknown substrate --------------------- DNA Metabolism - DNA replication, recombination, and repair - Restriction/modification - Chromosome-associated proteins --------------------- Transcription - Degradation of RNA - DNA-dependent RNA polymerase - Transcription factors - RNA processing -------------------- Translation - Amino acyl tRNA synthetases - Degradation of proteins, peptides, & glycopeptides - Protein modification - Ribosomal proteins: synthesis and modification - tRNA modification - Translation factors --------------------- Regulatory functions/General --------------------- Cell envelope - Surface structures - Murein sacculus & peptidoglycan Biosynthesis - Surface polysaccharides & lipopolysaccharides Biosynthesis - Polysaccharides Degradation - Other --------------------- Cellular Processes - Cell division - Chaperones - Detoxification - Protein & peptide secretion - Toxin production & resistance - Other --------------------- Other Categories - Adaptations and atypical conditions - Transposon-related functions - Other --------------------- Hypothetical/General tRNAs RNAs
	Strand:	Both Direct Reverse
	Orf Status	Any possible Putative Gene not a Putative Gene
	Gene Location is within:	and nucleotides (*)
	Orf Length is within:	and amino acids (*)
	Search similarity:
	COG Hit:	Any category ****** Information Storage And Processing ***** Translation, ribosomal structure and biogenesis Transcription DNA replication, recombination and repair ****** Cellular Processes ***** Cell division and chromosome partitioning Posttranslational modification, protein turnover, chaperones Cell envelope biogenesis, outer membrane Cell motility and secretion Inorganic ion transport and metabolism Signal transduction mechanisms ****** Metabolism ***** Energy production and conversion Carbohydrate transport and metabolism Amino acid transport and metabolism Nucleotide transport and metabolism Coenzyme metabolism Lipid metabolism ****** Poorly Characterized ***** General function prediction only Function unknown
	COG /Pathways and functional systems:
	Domain Pattern:	Any No Hit Pyrococcus Only Archaea Only Pyrococcus no Archaea Archaea & Bacteria Only Archae then Bacteria Archaea & Eucarya Only Archaea then Eucarya
	Search aa composition:	Values are expressed as offset from mean genome value
	(Charged - Polar):	Between: - -0.5 -0.4 -0.3 -0.2 -0.1 0.0 0.1 0.2 0.3 0.4 and : -0.5 -0.4 -0.3 -0.2 -0.1 0.0 0.1 0.2 0.3 0.4 -    (range : -0.47 - 0.33)
		Click here to enlarge
	Output Format:
	Return no more than:	25 50 100 500 Unlimited answers (*) Leave blank if seeking full genome range
	P. abyssi is 1765118 nucleotides long. Full P. abyssi genome screened for 30 aa. and more orfs using ATG, GTG and TTG start codons yielded 12540 orfs which are in the Orfs DataBase. Note: if a form input is left blank, then no matching is done on the field. Last revision on Fri Jan 23 2004 19:00:55 DataBase administrator Laboratoire de Biologie Moléculaire du Gène chez les Extrêmophiles.