Nitrosococcus halophilus Nc 4 plasmid pNHAL01, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Chromatiales; Chromatiaceae; Nitrosococcus.
Complete genome sequence of Nitrosococcus halophilus Nc4, a salt-adapted, aerobic obligate ammonia-oxidizing sulfur purple bacterium
Submitted (15-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\nCP001799.1.\nURL -- http://www.jgi.doe.gov\nJGI Project ID: 4082953\nSource DNA and bacteria available from Martin Klotz\n(martin.klotz@louisville.edu)\nContacts: Martin Klotz (martin.klotz@louisville.edu)\n David Bruce (microbe@cuba.jgi-psf.org)\nAnnotation done by JGI-ORNL and JGI-PGF\nFinishing done by JGI-LLNL\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 :: Nitrosococcus halophilus Nc4\nGOLD Stamp ID :: Gi04229\nOxygen Requirement :: Aerobic\nMotility :: Motile, chemotactic\nTemperature Range :: Mesophilic\nGram Staining :: Gram-\nBiotic Relationship :: Free living\nDiseases :: None\nHabitat :: Marine\nPhenotypes :: Obligate ammonia-oxidizing, Nitrifying,\n aerobic Denitrifying\nEnergy Source :: Chemolithotrophic\nCarbon Source :: Autotrophic (Calvin Benson Basham cycle)\n##Metadata-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/10/2023 02:02:00\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.4\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 3,960\nCDSs (total) :: 3,906\nGenes (coding) :: 3,843\nCDSs (with protein) :: 3,843\nGenes (RNA) :: 54\nrRNAs :: 2, 2, 2 (5S, 16S, 23S)\ncomplete rRNAs :: 2, 2, 2 (5S, 16S, 23S)\ntRNAs :: 44\nncRNAs :: 4\nPseudo Genes (total) :: 63\nCDSs (without protein) :: 63\nPseudo Genes (ambiguous residues) :: 0 of 63\nPseudo Genes (frameshifted) :: 22 of 63\nPseudo Genes (incomplete) :: 37 of 63\nPseudo Genes (internal stop) :: 13 of 63\nPseudo Genes (multiple problems) :: 7 of 63\nCRISPR Arrays :: 6\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_009805557.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013579.2
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020279714.1
class I SAM-dependent DNA methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_012340182.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_013028078.1
COORDINATES: similar to AA sequence:RefSeq:WP_004164104.1
COORDINATES: similar to AA sequence:RefSeq:WP_013221305.1
COORDINATES: similar to AA sequence:RefSeq:WP_019494680.1
COORDINATES: similar to AA sequence:RefSeq:WP_017841272.1
COORDINATES: similar to AA sequence:RefSeq:WP_004164080.1
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_002809353.1
helix-turn-helix transcriptional regulator
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF023168.2
COORDINATES: similar to AA sequence:RefSeq:WP_006960008.1
COORDINATES: similar to AA sequence:RefSeq:WP_005372452.1
COORDINATES: similar to AA sequence:RefSeq:WP_013032646.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006889831.1
COORDINATES: similar to AA sequence:RefSeq:WP_011330197.1
COORDINATES: similar to AA sequence:RefSeq:WP_004164068.1
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_002768162.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
type II toxin-antitoxin system HicA family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_013221948.1
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_017446059.1
GO:0004190 - aspartic-type endopeptidase activity [Evidence IEA]
GO:0008150 - biological_process [Evidence IEA]
TIGR02281 family clan AA aspartic protease
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_005375198.1
COORDINATES: similar to AA sequence:RefSeq:WP_005375199.1
COORDINATES: similar to AA sequence:RefSeq:WP_004164099.1
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_017735050.1
COORDINATES: similar to AA sequence:RefSeq:WP_002812282.1
COORDINATES: protein motif:HMM:NF021640.2
COORDINATES: protein motif:HMM:NF037888.2
HNH endonuclease signature motif containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013028132.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011920021.1
COORDINATES: protein motif:HMM:NF024106.2
COORDINATES: protein motif:HMM:NF025039.2
reverse transcriptase N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_001159683.1