Roseovarius indicus strain DSM 26383 plasmid pRIdsm_03, complete sequence.
Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; Roseobacteraceae; Roseovarius.
Genetic Globetrotter - A new plasmid hitch-hiking vast phylogenetic and geographic distances
Submitted (12-AUG-2018) Single Cell Genomics, Leibniz Institute DSMZ, Inhoffenstr. 8, Brunswick 38126, Germany
REFSEQ INFORMATION: The reference sequence is identical to\nCP031601.1.\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 Date :: FEB-2018\nAssembly Method :: HGAP v. 3\nAssembly Name :: DSMZ_RIdsm\nExpected Final Version :: yes\nGenome Coverage :: 100.0x\nSequencing Technology :: PacBio RS; Illumina\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/25/2023 02:27:30\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) :: 6,061\nCDSs (total) :: 6,008\nGenes (coding) :: 5,922\nCDSs (with protein) :: 5,922\nGenes (RNA) :: 53\nrRNAs :: 1, 1, 1 (5S, 16S, 23S)\ncomplete rRNAs :: 1, 1, 1 (5S, 16S, 23S)\ntRNAs :: 47\nncRNAs :: 3\nPseudo Genes (total) :: 86\nCDSs (without protein) :: 86\nPseudo Genes (ambiguous residues) :: 0 of 86\nPseudo Genes (frameshifted) :: 25 of 86\nPseudo Genes (incomplete) :: 60 of 86\nPseudo Genes (internal stop) :: 16 of 86\nPseudo Genes (multiple problems) :: 15 of 86\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
Qiliang Lai, Third Inst. Oceanography, State Oceanic Administration, Xiamen, China
COORDINATES: similar to AA sequence:RefSeq:WP_009503869.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_018001791.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
ParB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_019953310.1
COORDINATES: similar to AA sequence:RefSeq:WP_007817689.1
COORDINATES: similar to AA sequence:RefSeq:WP_009505369.1
COORDINATES: similar to AA sequence:RefSeq:WP_007803247.1
COORDINATES: similar to AA sequence:RefSeq:WP_013654751.1
COORDINATES: similar to AA sequence:RefSeq:WP_006643175.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503879.1
COORDINATES: similar to AA sequence:RefSeq:WP_009505363.1
GO:0042625 - ATPase-coupled ion transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_007803257.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820215.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820102.1
COORDINATES: similar to AA sequence:RefSeq:WP_008282917.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807542.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
ArdC-like ssDNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_020818725.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017183284.1
COORDINATES: similar to AA sequence:RefSeq:WP_015449375.1
COORDINATES: similar to AA sequence:RefSeq:WP_012115013.1
zincin-like metallopeptidase domain-containing protein
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_007120641.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187358.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807539.1
ParB/RepB/Spo0J family partition protein
COORDINATES: similar to AA sequence:RefSeq:WP_009820261.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187076.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187077.1
type II toxin-antitoxin system PrlF family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_007120648.1
type II toxin-antitoxin system YhaV family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_018076633.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0005886 - plasma membrane [Evidence IEA]
GO:0015416 - ABC-type phosphonate transporter activity [Evidence IEA]
GO:0015716 - organic phosphonate transport [Evidence IEA]
phosphonate ABC transporter, permease protein PhnE
COORDINATES: similar to AA sequence:RefSeq:WP_009238669.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0009897 - external side of plasma membrane [Evidence IEA]; GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0043168 - anion binding [Evidence IEA]; GO:0043225 - ATPase-coupled inorganic anion transmembrane transporter activity [Evidence IEA]
phosphate/phosphite/phosphonate ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_006023687.1
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing [Evidence IEA]; GO:0009898 - cytoplasmic side of plasma membrane [Evidence IEA]
GO:0015416 - ABC-type phosphonate transporter activity [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA]
phosphonate ABC transporter ATP-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_013294822.1
COORDINATES: protein motif:HMM:NF015431.2
COORDINATES: similar to AA sequence:RefSeq:WP_076612398.1
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_013221320.1
COORDINATES: similar to AA sequence:RefSeq:WP_011536522.1
sigma-54 dependent transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013896581.1
COORDINATES: similar to AA sequence:RefSeq:WP_012040798.1
nickel-dependent hydrogenase large subunit
COORDINATES: similar to AA sequence:RefSeq:WP_007015745.1
COORDINATES: similar to AA sequence:RefSeq:WP_007594378.1
COORDINATES: similar to AA sequence:RefSeq:WP_012599194.1
GO:0008233 - peptidase activity [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_007015749.1
COORDINATES: similar to AA sequence:RefSeq:WP_012592707.1
COORDINATES: similar to AA sequence:RefSeq:WP_012040805.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015752.1
GO:0005506 - iron ion binding [Evidence IEA]; GO:0051536 - iron-sulfur cluster binding [Evidence IEA]
GO:0016226 - iron-sulfur cluster assembly [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011536533.1
COORDINATES: similar to AA sequence:RefSeq:WP_007015754.1
GO:0003998 - acylphosphatase activity [Evidence IEA]
GO:0036211 - protein modification process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005863686.1
GO:0016530 - metallochaperone activity [Evidence IEA]; GO:0051082 - unfolded protein binding [Evidence IEA]
GO:0065003 - protein-containing complex assembly [Evidence IEA]
HypC/HybG/HupF family hydrogenase formation chaperone
COORDINATES: similar to AA sequence:RefSeq:WP_007796547.1
GO:0016530 - metallochaperone activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008886958.1
hydrogenase expression/formation protein HypE
COORDINATES: protein motif:HMM:NF013334.2
hydrogenase maturation nickel metallochaperone HypA
COORDINATES: similar to AA sequence:RefSeq:WP_007015761.1
GO:0016530 - metallochaperone activity [Evidence IEA]; GO:0000166 - nucleotide binding [Evidence IEA]
hydrogenase nickel incorporation protein HypB
COORDINATES: similar to AA sequence:RefSeq:WP_009503768.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327427.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187348.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807532.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187346.1
COORDINATES: similar to AA sequence:RefSeq:WP_009815530.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807529.1
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
rhomboid family intramembrane serine protease
COORDINATES: protein motif:HMM:NF012311.2
COORDINATES: similar to AA sequence:RefSeq:WP_006963521.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0016887 - ATP hydrolysis activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_009820257.1
COORDINATES: similar to AA sequence:RefSeq:WP_011536569.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120663.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009807938.1
relaxase/mobilization nuclease domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009807937.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_019965965.1
COORDINATES: protein motif:HMM:NF024867.2
COORDINATES: similar to AA sequence:RefSeq:WP_011655392.1
TerB N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_007011034.1
COORDINATES: similar to AA sequence:RefSeq:WP_011338082.1
GO:0005524 - ATP binding [Evidence IEA]; GO:0003676 - nucleic acid binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF017832.2
COORDINATES: similar to AA sequence:RefSeq:WP_009808070.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120671.1
COORDINATES: similar to AA sequence:RefSeq:WP_012187154.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807515.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327387.1
COORDINATES: similar to AA sequence:RefSeq:WP_011536592.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_009808064.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820232.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327379.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009494081.1
COORDINATES: similar to AA sequence:RefSeq:WP_007191299.1
COORDINATES: similar to AA sequence:RefSeq:WP_009807508.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008327373.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_009808058.1
COORDINATES: similar to AA sequence:RefSeq:WP_008327370.1
COORDINATES: similar to AA sequence:RefSeq:WP_008282965.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503806.1
COORDINATES: similar to AA sequence:RefSeq:WP_007120686.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_009815553.1
COORDINATES: similar to AA sequence:RefSeq:WP_009808043.1
COORDINATES: similar to AA sequence:RefSeq:WP_005861906.1
COORDINATES: similar to AA sequence:RefSeq:WP_010442288.1
COORDINATES: similar to AA sequence:RefSeq:WP_016845147.1
COORDINATES: similar to AA sequence:RefSeq:WP_005631488.1
COORDINATES: similar to AA sequence:RefSeq:WP_011771059.1
GO:0030288 - outer membrane-bounded periplasmic space [Evidence IEA]
GO:0003674 - molecular_function [Evidence IEA]
GO:0045861 - negative regulation of proteolysis [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018274875.1
COORDINATES: similar to AA sequence:RefSeq:WP_012641295.1
COORDINATES: similar to AA sequence:RefSeq:WP_005631495.1
COORDINATES: similar to AA sequence:RefSeq:WP_011339464.1
COORDINATES: similar to AA sequence:RefSeq:WP_008556092.1
COORDINATES: similar to AA sequence:RefSeq:WP_005631521.1
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_008556607.1
COORDINATES: similar to AA sequence:RefSeq:WP_009821400.1
COORDINATES: similar to AA sequence:RefSeq:WP_010441780.1
GO:0016887 - ATP hydrolysis activity [Evidence IEA]; GO:0005515 - protein binding [Evidence IEA]
GO:0006457 - protein folding [Evidence IEA]
60 kDa chaperone family; promotes refolding of misfolded polypeptides especially under stressful conditions; forms two stacked rings of heptamers to form a barrel-shaped 14mer; ends can be capped by GroES; misfolded proteins enter the barrel where they are refolded when GroES binds; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_008556108.1
COORDINATES: similar to AA sequence:RefSeq:WP_010442272.1
GO:0015385 - sodium:proton antiporter activity [Evidence IEA]
GO:1902600 - proton transmembrane transport [Evidence IEA]; GO:0006814 - sodium ion transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_018010711.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612399.1
incomplete; partial in the middle of a contig; missing N-terminus and C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF012738.2
GO:0055085 - transmembrane transport [Evidence IEA]
COORDINATES: protein motif:HMM:NF012235.2
COORDINATES: protein motif:HMM:NF024921.2
COORDINATES: protein motif:HMM:NF011990.0
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]
GO:0019700 - organic phosphonate catabolic process [Evidence IEA]
alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_012258834.1
COORDINATES: similar to AA sequence:RefSeq:WP_013076991.1
GO:0051539 - 4 iron, 4 sulfur cluster binding [Evidence IEA]; GO:0016829 - lyase activity [Evidence IEA]
alpha-D-ribose 1-methylphosphonate 5-phosphate C-P-lyase PhnJ
COORDINATES: similar to AA sequence:RefSeq:WP_013823311.1
GO:0019634 - organic phosphonate metabolic process [Evidence IEA]
carbon-phosphorus lyase complex subunit PhnI
COORDINATES: protein motif:HMM:NF017645.2
phosphonate C-P lyase system protein PhnH
COORDINATES: protein motif:HMM:TIGR02325.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
phosphonate metabolism transcriptional regulator PhnF
COORDINATES: similar to AA sequence:RefSeq:WP_008327468.1
COORDINATES: similar to AA sequence:RefSeq:WP_018001709.1
Mu transposase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009573528.1
COORDINATES: protein motif:HMM:NF018259.2
COORDINATES: similar to AA sequence:RefSeq:WP_005859475.1
COORDINATES: similar to AA sequence:RefSeq:WP_009819736.1
COORDINATES: similar to AA sequence:RefSeq:WP_018329048.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503864.1
COORDINATES: similar to AA sequence:RefSeq:WP_011331447.1
COORDINATES: similar to AA sequence:RefSeq:WP_009503866.1
AbrB/MazE/SpoVT family DNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_009827042.1
COORDINATES: similar to AA sequence:RefSeq:WP_009820070.1