Roseobacter denitrificans strain FDAARGOS_309 plasmid unnamed1, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Roseobacteraceae; Roseobacter.
FDA dAtabase for Regulatory Grade micrObial Sequences (FDA-ARGOS): Supporting development and validation of Infectious Disease Dx tests
Submitted (01-MAR-2018) Center for Devices and Radiological Health, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993-0002, USA
REFSEQ INFORMATION: The reference sequence is identical to\nCP027406.1.\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-Assembly-Data-START##\nAssembly Method :: CA v. 8.2\nGenome Coverage :: 409.207x\nSequencing Technology :: PacBio; Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 05/04/2023 04:21:46\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) :: 4,046\nCDSs (total) :: 4,002\nGenes (coding) :: 3,968\nCDSs (with protein) :: 3,968\nGenes (RNA) :: 44\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 38\nncRNAs :: 3\nPseudo Genes (total) :: 34\nCDSs (without protein) :: 34\nPseudo Genes (ambiguous residues) :: 0 of 34\nPseudo Genes (frameshifted) :: 18 of 34\nPseudo Genes (incomplete) :: 16 of 34\nPseudo Genes (internal stop) :: 10 of 34\nPseudo Genes (multiple problems) :: 9 of 34\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
Seaweed, Enteromorpha linza (coastal marine sediments), Aburatsubo Inlet, Australia
COORDINATES: similar to AA sequence:RefSeq:WP_009797930.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_013300279.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF012573.2
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF024565.2
COORDINATES: protein motif:HMM:NF024787.2
HNH endonuclease domain-containing protein
COORDINATES: protein motif:HMM:NF024867.2
COORDINATES: similar to AA sequence:RefSeq:WP_015917261.1
COORDINATES: similar to AA sequence:RefSeq:WP_006938682.1
COORDINATES: similar to AA sequence:RefSeq:WP_015460439.1
COORDINATES: protein motif:HMM:NF013094.2
COORDINATES: similar to AA sequence:RefSeq:WP_014853023.1
COORDINATES: protein motif:HMM:NF033611.0
COORDINATES: similar to AA sequence:RefSeq:WP_020039660.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007011034.1
COORDINATES: similar to AA sequence:RefSeq:WP_011338080.1
TerB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_013301526.1
COORDINATES: protein motif:HMM:NF016167.2
COORDINATES: similar to AA sequence:RefSeq:WP_009803631.1
COORDINATES: protein motif:HMM:NF018841.2
COORDINATES: similar to AA sequence:RefSeq:WP_009574265.1
COORDINATES: protein motif:HMM:NF013970.2
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_003456080.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009574266.1
COORDINATES: similar to AA sequence:RefSeq:WP_009504366.1
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012187063.1
COORDINATES: similar to AA sequence:RefSeq:WP_015494355.1
GO:0016798 - hydrolase activity, acting on glycosyl bonds [Evidence IEA]
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007121038.1
COORDINATES: protein motif:HMM:NF016957.2
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_011655374.1
COORDINATES: protein motif:HMM:NF019608.2
COORDINATES: protein motif:HMM:NF016491.2
COORDINATES: protein motif:HMM:NF016238.2
COORDINATES: protein motif:HMM:NF015487.2
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: similar to AA sequence:RefSeq:WP_011654614.1
COORDINATES: similar to AA sequence:RefSeq:WP_006203939.1
COORDINATES: similar to AA sequence:RefSeq:WP_011497995.1
COORDINATES: similar to AA sequence:RefSeq:WP_010442053.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0071705 - nitrogen compound transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_006935839.1
GO:0015501 - glutamate:sodium symporter activity [Evidence IEA]
GO:0015813 - L-glutamate transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF017773.2
COORDINATES: protein motif:HMM:NF013827.2
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
rhomboid family intramembrane serine protease
COORDINATES: protein motif:HMM:NF010424.0
The ATPase VirD4 is a core component of the VirB/VirD4 form of type IV secretion systems (T4SS), also known as type IVa secretion systems; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF015397.2
relaxase/mobilization nuclease domain-containing protein
COORDINATES: protein motif:HMM:NF010432.0
COORDINATES: protein motif:HMM:NF010423.0
COORDINATES: similar to AA sequence:RefSeq:WP_011536558.1
zincin-like metallopeptidase domain-containing protein
COORDINATES: protein motif:HMM:NF024242.2
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]; GO:0043565 - sequence-specific DNA binding [Evidence IEA]
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
helix-turn-helix transcriptional regulator
GO:0043565 - sequence-specific DNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020041537.1
COORDINATES: similar to AA sequence:RefSeq:WP_007198997.1
COORDINATES: similar to AA sequence:RefSeq:WP_015887681.1
COORDINATES: similar to AA sequence:RefSeq:WP_008280001.1
COORDINATES: similar to AA sequence:RefSeq:WP_019672972.1
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008197194.1
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_010504102.1
GO:0016722 - oxidoreductase activity, acting on metal ions [Evidence IEA]
DNA starvation/stationary phase protection protein Dps
COORDINATES: similar to AA sequence:RefSeq:WP_008887738.1
GO:0008080 - N-acetyltransferase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011299030.1
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015242302.1
GO:0051537 - 2 iron, 2 sulfur cluster binding [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008193986.1
GO:0016491 - oxidoreductase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013960776.1
COORDINATES: similar to AA sequence:RefSeq:WP_009817772.1
COORDINATES: similar to AA sequence:RefSeq:WP_008232186.1
COORDINATES: protein motif:HMM:NF017128.2
COORDINATES: similar to AA sequence:RefSeq:WP_007692755.1
GO:0004540 - ribonuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_013896367.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_010400636.1
COORDINATES: similar to AA sequence:RefSeq:WP_012115011.1
COORDINATES: protein motif:HMM:TIGR00180.1
GO:0007059 - chromosome segregation [Evidence IEA]; GO:0000910 - cytokinesis [Evidence IEA]
ParB/RepB/Spo0J family partition protein
COORDINATES: protein motif:HMM:NF018871.2
COORDINATES: similar to AA sequence:RefSeq:WP_007815827.1
COORDINATES: similar to AA sequence:RefSeq:WP_013959856.1
COORDINATES: similar to AA sequence:RefSeq:WP_009309957.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_052096176.1
internal stop; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018240503.1
COORDINATES: similar to AA sequence:RefSeq:WP_009468356.1
COORDINATES: similar to AA sequence:RefSeq:WP_019013976.1