Arsenophonus nasoniae strain FIN plasmid pArsFIN2, complete sequence.
Arsenophonus nasoniae (son-killer infecting Nasonia vitripennis)
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Morganellaceae; Arsenophonus.
Long-read sequencing reveals hyperdense prophage content in a complex bacterial symbiont genome
Submitted (29-MAR-2019) Evolution, Ecology and Behaviour, University of Liverpool, Crown Street, Biosciences building, Liverpool L69 7ZB, United Kingdom
REFSEQ INFORMATION: The reference sequence is identical to\nCP038614.1.\nAnnotated using prokka 1.12-beta from\nhttps://github.com/tseemann/prokka.\nBacteria and source DNA available from Prof Greg Hurst, Institute\nof Integrative Biology, University of Liverpool.\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 :: 2018\nAssembly Method :: Unicycler v. 0.4.5\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 169.0x\nSequencing Technology :: Oxford Nanopore MiniION; PacBio RSII;\n Illumina MiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/25/2023 01:21:09\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) :: 5,421\nCDSs (total) :: 5,317\nGenes (coding) :: 4,929\nCDSs (with protein) :: 4,929\nGenes (RNA) :: 104\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 70\nncRNAs :: 12\nPseudo Genes (total) :: 388\nCDSs (without protein) :: 388\nPseudo Genes (ambiguous residues) :: 0 of 388\nPseudo Genes (frameshifted) :: 199 of 388\nPseudo Genes (incomplete) :: 170 of 388\nPseudo Genes (internal stop) :: 85 of 388\nPseudo Genes (multiple problems) :: 61 of 388\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_015981317.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
Rpn family recombination-promoting nuclease/putative transposase
COORDINATES: similar to AA sequence:RefSeq:WP_016857296.1
GO:0003905 - alkylbase DNA N-glycosylase activity [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]
GO:0006284 - base-excision repair [Evidence IEA]
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF016847.2
GO:0004803 - transposase activity [Evidence IEA]
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_076612135.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_017188841.1
COORDINATES: protein motif:HMM:NF015831.2
COORDINATES: protein motif:HMM:NF040300.1
COORDINATES: similar to AA sequence:RefSeq:WP_016247728.1
COORDINATES: similar to AA sequence:RefSeq:WP_004144477.1
COORDINATES: protein motif:HMM:NF024738.2
topoisomerase C-terminal repeat-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_001293133.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
H-NS family nucleoid-associated regulatory protein
COORDINATES: similar to AA sequence:RefSeq:WP_004256366.1
GO:0006807 - nitrogen compound metabolic process [Evidence IEA]
nitrilase-related carbon-nitrogen hydrolase
COORDINATES: protein motif:HMM:NF024698.2
COORDINATES: similar to AA sequence:RefSeq:WP_011816254.1
COORDINATES: protein motif:HMM:NF020037.2
PAS and helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF037421.2
COORDINATES: protein motif:HMM:NF025677.2
transposase zinc-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004152394.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015873870.1
COORDINATES: similar to AA sequence:RefSeq:WP_011785204.1
internal stop; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF022500.2
COORDINATES: protein motif:HMM:NF033546.1
frameshifted; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013828.2
COORDINATES: similar to AA sequence:RefSeq:WP_006954077.1
COORDINATES: protein motif:HMM:NF024728.2
COORDINATES: similar to AA sequence:RefSeq:WP_014657458.1
COORDINATES: protein motif:HMM:NF016703.2
COORDINATES: protein motif:HMM:NF026929.2
COORDINATES: protein motif:HMM:NF013601.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_011279176.1
COORDINATES: similar to AA sequence:RefSeq:WP_004929550.1
COORDINATES: similar to AA sequence:RefSeq:WP_004722065.1
GO:0015074 - DNA integration [Evidence IEA]
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_004904218.1
COORDINATES: similar to AA sequence:RefSeq:WP_013184818.1
COORDINATES: similar to AA sequence:RefSeq:WP_016192069.1
COORDINATES: protein motif:HMM:NF013933.2
COORDINATES: similar to AA sequence:RefSeq:WP_012368205.1
GO:0006260 - DNA replication [Evidence IEA]
frameshifted; 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:NF017640.2
COORDINATES: similar to AA sequence:RefSeq:WP_013184827.1
COORDINATES: similar to AA sequence:RefSeq:WP_000198539.1
COORDINATES: similar to AA sequence:RefSeq:WP_017154883.1
COORDINATES: similar to AA sequence:RefSeq:WP_017154806.1
COORDINATES: similar to AA sequence:RefSeq:WP_006704154.1
COORDINATES: similar to AA sequence:RefSeq:WP_000191998.1
COORDINATES: protein motif:HMM:NF016255.2
COORDINATES: similar to AA sequence:RefSeq:WP_017047108.1
type I restriction endonuclease subunit R
COORDINATES: similar to AA sequence:RefSeq:WP_013445466.1
GO:0006304 - DNA modification [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_004071734.1
GO:0015666 - restriction endodeoxyribonuclease activity [Evidence IEA]; GO:0009007 - site-specific DNA-methyltransferase (adenine-specific) activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]; GO:0009307 - DNA restriction-modification system [Evidence IEA]
type I restriction-modification system subunit M
COORDINATES: similar to AA sequence:RefSeq:WP_011386370.1
COORDINATES: similar to AA sequence:RefSeq:WP_011279233.1
Rop family plasmid primer RNA-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_016240486.1
COORDINATES: similar to AA sequence:RefSeq:WP_015874496.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_016857298.1
COORDINATES: protein motif:HMM:NF012422.2
COORDINATES: similar to AA sequence:RefSeq:WP_015632948.1
COORDINATES: similar to AA sequence:RefSeq:WP_011411299.1
COORDINATES: similar to AA sequence:RefSeq:WP_012737910.1
hydantoinase/oxoprolinase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_006704307.1
COORDINATES: protein motif:HMM:NF018726.2
GO:0005524 - ATP binding [Evidence IEA]; GO:0003677 - DNA binding [Evidence IEA]; GO:0003678 - DNA helicase activity [Evidence IEA]; GO:0016818 - hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides [Evidence IEA]
conjugative transfer relaxase/helicase TraI
COORDINATES: similar to AA sequence:RefSeq:WP_002950442.1
type III secretion system effector inositol phosphate phosphatase
COORDINATES: protein motif:HMM:NF019441.2
COORDINATES: similar to AA sequence:RefSeq:WP_001568107.1
conjugal transfer relaxosome DNA-binding protein TraM
COORDINATES: similar to AA sequence:RefSeq:WP_008324168.1
transglycosylase SLT domain-containing protein
programmed frameshift; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF016629.2
COORDINATES: protein motif:HMM:NF018148.2
COORDINATES: protein motif:HMM:TIGR01784.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013003.2
COORDINATES: similar to AA sequence:RefSeq:WP_000628840.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612362.1
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:NF018714.2
COORDINATES: similar to AA sequence:RefSeq:WP_017356992.1
COORDINATES: protein motif:HMM:NF012485.2
COORDINATES: similar to AA sequence:RefSeq:WP_015874571.1
COORDINATES: similar to AA sequence:RefSeq:WP_006081435.1
COORDINATES: protein motif:HMM:NF017605.2
COORDINATES: similar to AA sequence:RefSeq:WP_000712390.1
COORDINATES: protein motif:HMM:NF016998.2
phage/plasmid replication protein, II/X family
COORDINATES: similar to AA sequence:RefSeq:WP_009092619.1
phosphate-starvation-inducible PsiE family protein
COORDINATES: similar to AA sequence:RefSeq:WP_002212220.1
COORDINATES: similar to AA sequence:RefSeq:WP_020317119.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_001595120.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_016857956.1
type II secretion system F family protein
COORDINATES: similar to AA sequence:RefSeq:WP_001080803.1
COORDINATES: similar to AA sequence:RefSeq:WP_000538728.1
COORDINATES: similar to AA sequence:RefSeq:WP_000788525.1
COORDINATES: similar to AA sequence:RefSeq:WP_016247943.1
COORDINATES: similar to AA sequence:RefSeq:WP_009874495.1
COORDINATES: similar to AA sequence:RefSeq:WP_019624938.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611197.1
COORDINATES: protein motif:HMM:NF020068.2
COORDINATES: protein motif:HMM:NF015803.2
ShlB/FhaC/HecB family hemolysin secretion/activation protein
COORDINATES: similar to AA sequence:RefSeq:WP_012772808.1
filamentous hemagglutinin N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF033538.1
COORDINATES: similar to AA sequence:RefSeq:WP_012105721.1
GO:0019812 - type I site-specific deoxyribonuclease complex [Evidence IEA]
GO:0009035 - type I site-specific deoxyribonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
HsdR family type I site-specific deoxyribonuclease
COORDINATES: similar to AA sequence:RefSeq:WP_012105720.1
COORDINATES: similar to AA sequence:RefSeq:WP_006662569.1
COORDINATES: similar to AA sequence:RefSeq:WP_005759576.1
COORDINATES: similar to AA sequence:RefSeq:WP_006322813.1
COORDINATES: similar to AA sequence:RefSeq:WP_016260098.1
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_017173693.1
COORDINATES: similar to AA sequence:RefSeq:WP_003144688.1
COORDINATES: protein motif:HMM:NF013235.2
LuxR C-terminal-related transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_013141615.1
COORDINATES: similar to AA sequence:RefSeq:WP_013512757.1
COORDINATES: similar to AA sequence:RefSeq:WP_013521176.1
type II toxin-antitoxin system YafQ family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_014003226.1
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: protein motif:HMM:NF018125.2
COORDINATES: protein motif:HMM:NF016148.2
COORDINATES: protein motif:HMM:NF021494.2
COORDINATES: similar to AA sequence:RefSeq:WP_011147117.1
COORDINATES: similar to AA sequence:RefSeq:WP_019076906.1
COORDINATES: protein motif:HMM:NF024659.2
COORDINATES: similar to AA sequence:RefSeq:WP_017348369.1
COORDINATES: similar to AA sequence:RefSeq:WP_010400642.1
COORDINATES: protein motif:HMM:NF023291.2
internal stop; incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
class I SAM-dependent DNA methyltransferase
COORDINATES: similar to AA sequence:RefSeq:WP_014539784.1
GO:0022857 - transmembrane transporter activity [Evidence IEA]
GO:0055085 - transmembrane transport [Evidence IEA]
glycine betaine/L-proline transporter ProP
COORDINATES: similar to AA sequence:RefSeq:WP_011920327.1
COORDINATES: protein motif:HMM:NF022241.2
plasmid partitioning/stability family protein
COORDINATES: similar to AA sequence:RefSeq:WP_001687089.1