Nitrosococcus oceani ATCC 19707 plasmid A, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Chromatiales; Chromatiaceae; Nitrosococcus.
Complete sequence of Plasmid A of Nitrosococcus oceani ATCC 19707
Submitted (21-SEP-2005) US DOE Joint Genome Institute, 2400 Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP000126.1.\nURL -- http://www.jgi.doe.gov\nSource DNA available from Dan Arp (arpd@bcc.orst.edu)\nBacteria available from ATCC: ATCC 19707\nWhole genome sequencing and draft assembly at JGI-PGF\nFinishing done by JGI-LLNL\nQuality assurance done by JGI-Stanford\nAnnotation done by JGI-ORNL and JGI-PGF\nContacts: Paul Richardson (microbes@cuba.jgi-psf.org)\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 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##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 04/27/2023 01:28:34\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) :: 3,343\nCDSs (total) :: 3,288\nGenes (coding) :: 3,237\nCDSs (with protein) :: 3,237\nGenes (RNA) :: 55\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 45\nncRNAs :: 4\nPseudo Genes (total) :: 51\nCDSs (without protein) :: 51\nPseudo Genes (ambiguous residues) :: 0 of 51\nPseudo Genes (frameshifted) :: 22 of 51\nPseudo Genes (incomplete) :: 28 of 51\nPseudo Genes (internal stop) :: 18 of 51\nPseudo Genes (multiple problems) :: 13 of 51\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_013028099.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011330185.1
COORDINATES: similar to AA sequence:RefSeq:WP_004164049.1
COORDINATES: similar to AA sequence:RefSeq:WP_004164094.1
COORDINATES: similar to AA sequence:RefSeq:WP_004164075.1
toxin-antitoxin system HicB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_004164102.1
GO:0003729 - mRNA binding [Evidence IEA]
type II toxin-antitoxin system HicA family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_013028104.1
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_013028106.1
COORDINATES: similar to AA sequence:RefSeq:WP_004164089.1
GO:0015627 - type II protein secretion system complex [Evidence IEA]
GO:0015628 - protein secretion by the type II secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004164063.1
COORDINATES: similar to AA sequence:RefSeq:WP_004164064.1
COORDINATES: similar to AA sequence:RefSeq:WP_004164110.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004164088.1
COORDINATES: similar to AA sequence:RefSeq:WP_004164059.1
COORDINATES: similar to AA sequence:RefSeq:WP_004164099.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
GO:0007059 - chromosome segregation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004164060.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_013028117.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013221944.1
COORDINATES: similar to AA sequence:RefSeq:WP_004164090.1
COORDINATES: similar to AA sequence:RefSeq:WP_013032910.1
COORDINATES: similar to AA sequence:RefSeq:WP_004164079.1
COORDINATES: similar to AA sequence:RefSeq:WP_004164081.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF017243.2
COORDINATES: similar to AA sequence:RefSeq:WP_004164062.1
GO:0003953 - NAD+ nucleosidase activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
GO:0007165 - signal transduction [Evidence IEA]
toll/interleukin-1 receptor domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004164076.1
COORDINATES: similar to AA sequence:RefSeq:WP_004164053.1
COORDINATES: similar to AA sequence:RefSeq:WP_013034255.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013034256.1
COORDINATES: similar to AA sequence:RefSeq:WP_002814337.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016786753.1
COORDINATES: similar to AA sequence:RefSeq:WP_004164074.1
COORDINATES: similar to AA sequence:RefSeq:WP_005740025.1
COORDINATES: similar to AA sequence:RefSeq:WP_004164104.1
COORDINATES: similar to AA sequence:RefSeq:WP_004164066.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004521 - endoribonuclease activity [Evidence IEA]; GO:0003723 - RNA binding [Evidence IEA]
type II toxin-antitoxin system PemK/MazF family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_004164082.1
COORDINATES: similar to AA sequence:RefSeq:WP_012972373.1
COORDINATES: similar to AA sequence:RefSeq:WP_011330195.1
COORDINATES: similar to AA sequence:RefSeq:WP_004164080.1
COORDINATES: similar to AA sequence:RefSeq:WP_013221934.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_004164047.1
COORDINATES: similar to AA sequence:RefSeq:WP_004164067.1
COORDINATES: similar to AA sequence:RefSeq:WP_004164073.1
COORDINATES: similar to AA sequence:RefSeq:WP_011330197.1