Arsenophonus nasoniae strain FIN plasmid pArsFIN5, 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\nCP038617.1.\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+.
conjugal transfer relaxosome DNA-binding protein TraM
COORDINATES: similar to AA sequence:RefSeq:WP_004966240.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
transglycosylase SLT domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014657458.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612135.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF033546.1
COORDINATES: similar to AA sequence:RefSeq:WP_006322813.1
COORDINATES: similar to AA sequence:RefSeq:WP_000165985.1
Rop family plasmid primer RNA-binding protein
COORDINATES: protein motif:HMM:NF022241.2
plasmid partitioning/stability family protein
COORDINATES: similar to AA sequence:RefSeq:WP_001687089.1
COORDINATES: protein motif:HMM:NF016255.2
COORDINATES: similar to AA sequence:RefSeq:WP_015873870.1
Rpn family recombination-promoting nuclease/putative transposase
COORDINATES: similar to AA sequence:RefSeq:WP_004733699.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_006703980.1
COORDINATES: similar to AA sequence:RefSeq:WP_004144477.1
COORDINATES: protein motif:HMM:NF025677.2
transposase zinc-binding domain-containing protein
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
LuxR C-terminal-related transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_004929550.1
COORDINATES: similar to AA sequence:RefSeq:WP_000559543.1
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_001419705.1
COORDINATES: similar to AA sequence:RefSeq:WP_007203269.1
COORDINATES: protein motif:HMM:NF013235.2
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:TIGR00616.1
GO:0006259 - DNA metabolic process [Evidence IEA]
COORDINATES: protein motif:HMM:NF013884.2
COORDINATES: similar to AA sequence:RefSeq:WP_016241765.1
COORDINATES: similar to AA sequence:RefSeq:WP_000002046.1
COORDINATES: protein motif:HMM:NF022494.2
COORDINATES: protein motif:HMM:NF037331.2
Gp138 family membrane-puncturing spike protein
COORDINATES: similar to AA sequence:RefSeq:WP_010846150.1
COORDINATES: protein motif:HMM:NF024659.2
COORDINATES: similar to AA sequence:RefSeq:WP_019076906.1
COORDINATES: similar to AA sequence:RefSeq:WP_011147117.1
COORDINATES: protein motif:HMM:NF021494.2
COORDINATES: protein motif:HMM:NF016148.2
COORDINATES: protein motif:HMM:NF018125.2
COORDINATES: similar to AA sequence:RefSeq:WP_004085174.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_010893244.1
COORDINATES: similar to AA sequence:RefSeq:WP_013512757.1
COORDINATES: similar to AA sequence:RefSeq:WP_006812856.1
ogr/Delta-like zinc finger family protein
COORDINATES: similar to AA sequence:RefSeq:WP_013184792.1
COORDINATES: similar to AA sequence:RefSeq:WP_006657265.1
COORDINATES: protein motif:HMM:NF018260.2
COORDINATES: similar to AA sequence:RefSeq:WP_006657268.1
COORDINATES: similar to AA sequence:RefSeq:WP_004904031.1
GO:0044423 - virion component [Evidence IEA]
GO:0005198 - structural molecule activity [Evidence IEA]
GO:0016032 - viral process [Evidence IEA]
COORDINATES: protein motif:HMM:NF023351.2
inverse autotransporter beta-barrel domain-containing protein
COORDINATES: protein motif:HMM:NF025079.2
COORDINATES: protein motif:HMM:NF016759.2
type III secretion system translocon subunit SctE
COORDINATES: similar to AA sequence:RefSeq:WP_006705581.1
COORDINATES: similar to AA sequence:RefSeq:WP_006250155.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005165738.1
zonular occludens toxin domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_000467082.1
COORDINATES: similar to AA sequence:RefSeq:WP_014655990.1
COORDINATES: similar to AA sequence:RefSeq:WP_000566297.1
GO:0006260 - DNA replication [Evidence IEA]
phage/plasmid replication protein, II/X family
COORDINATES: similar to AA sequence:RefSeq:WP_014655995.1
COORDINATES: protein motif:HMM:NF017605.2
COORDINATES: protein motif:HMM:NF016847.2
COORDINATES: protein motif:HMM:NF024991.2
COORDINATES: similar to AA sequence:RefSeq:WP_011192680.1
COORDINATES: similar to AA sequence:RefSeq:WP_004717867.1
COORDINATES: similar to AA sequence:RefSeq:WP_011815933.1
GO:0009401 - phosphoenolpyruvate-dependent sugar phosphotransferase system [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_012468331.1
GO:0004386 - helicase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_014888268.1
COORDINATES: protein motif:HMM:NF013618.2
lytic transglycosylase domain-containing protein
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001760564.1
COORDINATES: similar to AA sequence:RefSeq:WP_001760566.1
COORDINATES: similar to AA sequence:RefSeq:WP_006662569.1
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_012105720.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611985.1
GO:0015074 - DNA integration [Evidence IEA]
integrase core domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008324121.1
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_006954077.1
COORDINATES: similar to AA sequence:RefSeq:YP_005229693.1
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: similar to AA sequence:RefSeq:WP_013609534.1
conjugal transfer mating-pair stabilization protein TraG
COORDINATES: similar to AA sequence:RefSeq:WP_001568075.1
type IV conjugative transfer system coupling protein TraD
COORDINATES: similar to AA sequence:RefSeq:WP_004966169.1
conjugative transfer relaxase/helicase TraI
COORDINATES: protein motif:HMM:NF015386.2