Arsenophonus nasoniae strain FIN plasmid pArsFIN8, 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\nCP038620.1.\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+.
COORDINATES: protein motif:HMM:NF033538.1
GO:0004803 - transposase activity [Evidence IEA]
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:WP_014657458.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_004144477.1
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:NF023351.2
COORDINATES: protein motif:HMM:NF025677.2
transposase zinc-binding domain-containing protein
COORDINATES: protein motif:HMM:NF025085.2
COORDINATES: protein motif:HMM:NF013618.2
transglycosylase SLT domain-containing protein
COORDINATES: protein motif:HMM:NF017124.2
GO:0045893 - positive regulation of DNA-templated transcription [Evidence IEA]; GO:1902208 - regulation of bacterial-type flagellum assembly [Evidence IEA]
COORDINATES: protein motif:HMM:NF011458.0
conjugal transfer mating pair stabilization protein TraN
COORDINATES: similar to AA sequence:RefSeq:WP_006708696.1
COORDINATES: similar to AA sequence:RefSeq:WP_011410629.1
Rpn family recombination-promoting nuclease/putative transposase
COORDINATES: protein motif:HMM:NF016255.2
COORDINATES: similar to AA sequence:RefSeq:WP_000628840.1
COORDINATES: similar to AA sequence:RefSeq:WP_076612135.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_004247212.1
type II toxin-antitoxin system VapB family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_009112507.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: protein motif:HMM:NF012798.2
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: protein motif:HMM:NF021981.2
GO:0004252 - serine-type endopeptidase activity [Evidence IEA]
GO:0009306 - protein secretion [Evidence IEA]; GO:0006465 - signal peptide processing [Evidence IEA]
COORDINATES: protein motif:HMM:NF016362.2
COORDINATES: similar to AA sequence:RefSeq:WP_011409936.1
COORDINATES: protein motif:HMM:NF020037.2
helix-turn-helix transcriptional regulator
COORDINATES: protein motif:HMM:NF024642.2
COORDINATES: similar to AA sequence:RefSeq:WP_007372215.1
TraA family conjugative transfer protein
COORDINATES: protein motif:HMM:NF024853.2
COORDINATES: protein motif:HMM:NF012422.2
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
LuxR C-terminal-related transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_020314634.1
COORDINATES: similar to AA sequence:RefSeq:WP_010905402.1
COORDINATES: similar to AA sequence:RefSeq:WP_000484486.1
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_011147281.1
COORDINATES: similar to AA sequence:RefSeq:WP_006384705.1
COORDINATES: similar to AA sequence:RefSeq:WP_011092230.1
COORDINATES: similar to AA sequence:RefSeq:WP_002121575.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873870.1
COORDINATES: protein motif:HMM:NF018148.2
COORDINATES: similar to AA sequence:RefSeq:WP_004920922.1
COORDINATES: protein motif:HMM:NF016629.2
COORDINATES: similar to AA sequence:RefSeq:WP_012304635.1
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: protein motif:HMM:NF013579.2
GO:0006304 - DNA modification [Evidence IEA]
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: protein motif:HMM:NF022241.2
plasmid partitioning/stability family protein
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
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [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:NF012321.2
COORDINATES: protein motif:HMM:NF025105.2
COORDINATES: protein motif:HMM:NF017892.2
COORDINATES: protein motif:HMM:NF019530.2
conjugal transfer protein TraG N-terminal domain-containing protein
COORDINATES: protein motif:HMM:NF015489.2
GO:0015643 - toxic substance binding [Evidence IEA]
GO:0030153 - bacteriocin immunity [Evidence IEA]
colicin E1 family microcin immunity protein
COORDINATES: protein motif:HMM:NF013211.2
GO:0019835 - cytolysis [Evidence IEA]; GO:0050829 - defense response to Gram-negative bacterium [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_015873553.1
COORDINATES: similar to AA sequence:RefSeq:WP_000879771.1
COORDINATES: similar to AA sequence:RefSeq:WP_000262326.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_001760566.1