Ammonifex degensii KC4 plasmid pADEG01, complete sequence.
Bacteria; Bacillota; Clostridia; Thermoanaerobacterales; Thermoanaerobacteraceae; Ammonifex.
Complete sequence of plasmid of Ammonifex degensii KC4
Submitted (02-OCT-2009) US DOE Joint Genome Institute, 2800 Mitchell Drive B310, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP001786.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4003801\nSource DNA available from DSMZ: DSM 10501 (http://www.dsmz.de)\nContacts: Cheryl Kerfeld (CKerfeld@lbl.gov)\n David Bruce (microbe@cuba.jgi-psf.org)\nAnnotation done by JGI-ORNL and JGI-PGF\nUCLA undergraduates in LS187 contributed to the sequencing and\nanalysis of this genome.\nAlso, students and faculty at the following schools participated in\nanalysis of the A. degensii genome: Austin College (Professor\nKelynne Reed); Bowling Green State University (Professor Zhaohui\nXu); University of Missouri-Columbia, Professor Sharyn Freyermuth);\nThe University of St. Thomas (Professor Jayna L. Ditty); St. Cloud\nState University (Professor Christopher Kvaal); University of\nNebraska (Professor Cheryl Bailey); University of Southern\nMississippi (Professor Sabine Heinhorst); (University of South\nFlorida (Professor Kathleen Scott); Michigan State University\n(Professor Robert Britton); University of California, Los Angeles\n(Professor Erin Sanders-Lorenz); Northern Illinois University\n(Professor Rick Johns); Hiram College (Professors Stuart Gordon and\nBrad Goodner)\nFinishing done by JGI-LANL\nFinished microbial genomes have been curated to close all gaps with\ngreater than 98% coverage of at least two independent clones. Each\nbase pair has a minimum q (quality) value of 30 and the total error\nrate is less than one per 50000.\nThe JGI and collaborators endorse the principles for the\ndistribution and use of large scale sequencing data adopted by the\nlarger genome sequencing community and urge users of this data to\nfollow them. it is our intention to publish the work of this\nproject in a timely fashion and we welcome collaborative\ninteraction on the project and analysis.\n(http://www.genome.gov/page.cfm?pageID=10506376).\nThe annotation was added by the NCBI Prokaryotic Genome Annotation\nPipeline (PGAP). Information about PGAP can be found here:\nhttps://www.ncbi.nlm.nih.gov/genome/annotation_prok/\n\n##Metadata-START##\nOrganism Display Name :: Ammonifex degensii KC4\nCulture Collection ID :: DSM 10501\nGOLD Stamp ID :: Gi00784\nGreengenes ID :: 13731\nIsolation Site :: Neutral volcanic hot spring\nOxygen Requirement :: Anaerobe\nCell Shape :: Rod-shaped\nMotility :: Motile\nTemperature Range :: Thermophile\nTemperature Optimum :: 70C\nGram Staining :: gram-\nBiotic Relationship :: Free living\nDiseases :: None\nHabitat :: Fresh water, Hot spring\nEnergy Source :: Chemolithoautotroph\n##Metadata-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/09/2023 08:54:26\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 2,250\nCDSs (total) :: 2,193\nGenes (coding) :: 2,158\nCDSs (with protein) :: 2,158\nGenes (RNA) :: 57\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 4\nPseudo Genes (total) :: 35\nCDSs (without protein) :: 35\nPseudo Genes (ambiguous residues) :: 0 of 35\nPseudo Genes (frameshifted) :: 13 of 35\nPseudo Genes (incomplete) :: 24 of 35\nPseudo Genes (internal stop) :: 3 of 35\nPseudo Genes (multiple problems) :: 5 of 35\nCRISPR Arrays :: 8\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: protein motif:HMM:NF019450.2
Derived by automated computational analysis using gene prediction method: Protein Homology.
copper amine oxidase N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF015380.2
COORDINATES: protein motif:HMM:NF025616.2
COORDINATES: similar to AA sequence:RefSeq:WP_011392209.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF024803.2
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012818242.1
COORDINATES: similar to AA sequence:RefSeq:WP_012818243.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_011928453.1
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF024776.2
COORDINATES: similar to AA sequence:RefSeq:WP_012302603.1
COORDINATES: protein motif:HMM:TIGR01764.1
COORDINATES: protein motif:HMM:NF020419.2
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: protein motif:HMM:NF024734.2
type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013822664.1
COORDINATES: similar to AA sequence:RefSeq:WP_004399083.1
GO:0004521 - endoribonuclease activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
putative toxin-antitoxin system toxin component, PIN family
COORDINATES: similar to AA sequence:RefSeq:WP_011928482.1
GO:0110001 - toxin-antitoxin complex [Evidence IEA]
type II toxin-antitoxin system Phd/YefM family antitoxin