Arsenophonus nasoniae strain FIN plasmid pArsFIN3, 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\nCP038615.1.\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: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_016257341.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
PBSX family phage terminase large subunit
COORDINATES: similar to AA sequence:RefSeq:WP_013512757.1
COORDINATES: similar to AA sequence:RefSeq:WP_010893244.1
COORDINATES: similar to AA sequence:RefSeq:WP_004085174.1
type II toxin-antitoxin system RelE/ParE family toxin
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_004144477.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: protein motif:HMM:NF015776.2
GO:0006259 - DNA metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_019214504.1
COORDINATES: similar to AA sequence:RefSeq:WP_017549891.1
COORDINATES: protein motif:HMM:NF016847.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0004803 - transposase activity [Evidence IEA]
GO:0006313 - transposition, DNA-mediated [Evidence IEA]
COORDINATES: protein motif:HMM:NF025677.2
transposase zinc-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_006954077.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_014657458.1
COORDINATES: similar to AA sequence:RefSeq:WP_008807690.1
GO:0008951 - palmitoleoyl [acyl-carrier-protein]-dependent acyltransferase activity [Evidence IEA]
GO:0036104 - Kdo2-lipid A biosynthetic process [Evidence IEA]; GO:0009409 - response to cold [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.
kdo(2)-lipid IV(A) palmitoleoyltransferase
frameshifted; 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_076612135.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006708696.1
COORDINATES: similar to AA sequence:RefSeq:WP_017726418.1
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF015218.2
COORDINATES: similar to AA sequence:RefSeq:WP_006704782.1
COORDINATES: protein motif:HMM:NF013828.2
COORDINATES: similar to AA sequence:RefSeq:WP_006809777.1
COORDINATES: protein motif:HMM:NF018148.2
COORDINATES: protein motif:HMM:NF022241.2
plasmid partitioning/stability family protein
COORDINATES: similar to AA sequence:RefSeq:WP_001419705.1
COORDINATES: similar to AA sequence:RefSeq:WP_003144688.1
COORDINATES: protein motif:HMM:NF013235.2
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
RepB family plasmid replication initiator protein
COORDINATES: protein motif:HMM:NF017542.2
GO:0006260 - DNA replication [Evidence IEA]; GO:0006276 - plasmid maintenance [Evidence IEA]
COORDINATES: protein motif:HMM:NF012422.2
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF024096.2
PD-(D/E)XK nuclease-like domain-containing protein
COORDINATES: protein motif:HMM:NF016876.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
LuxR C-terminal-related transcriptional regulator
COORDINATES: protein motif:HMM:NF021467.2
COORDINATES: protein motif:HMM:NF024659.2
COORDINATES: similar to AA sequence:RefSeq:WP_010846150.1
COORDINATES: protein motif:HMM:NF023291.2
COORDINATES: protein motif:HMM:NF037331.2
Gp138 family membrane-puncturing spike protein
COORDINATES: protein motif:HMM:NF022494.2
COORDINATES: protein motif:HMM:NF019126.2
COORDINATES: protein motif:HMM:NF025622.2
glucosyltransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_000703656.1
COORDINATES: similar to AA sequence:RefSeq:WP_011199842.1
COORDINATES: protein motif:HMM:TIGR00616.1
COORDINATES: similar to AA sequence:RefSeq:WP_000007848.1
COORDINATES: similar to AA sequence:RefSeq:WP_020322885.1
GO:0016756 - glutathione gamma-glutamylcysteinyltransferase activity [Evidence IEA]; GO:0046872 - metal ion binding [Evidence IEA]
GO:0046938 - phytochelatin biosynthetic process [Evidence IEA]; GO:0010038 - response to metal ion [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_005356644.1
COORDINATES: similar to AA sequence:RefSeq:WP_004146678.1
COORDINATES: similar to AA sequence:RefSeq:WP_015971229.1
COORDINATES: similar to AA sequence:RefSeq:WP_004243368.1
COORDINATES: similar to AA sequence:RefSeq:WP_006661260.1
COORDINATES: similar to AA sequence:RefSeq:WP_017628366.1