Arsenophonus apicola strain ArsBeeUS plasmid pArsBee5, complete sequence.
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Morganellaceae; Arsenophonus.
Culture and genomic analysis of Arsenophonus apicola sp. nov. isolated from the honeybee Apis mellifera
Submitted (27-SEP-2021) Evolution, Ecology and Behaviour, University of Liverpool, Crown Street, Biosciences building, Liverpool L69 7ZB, United Kingdom
REFSEQ INFORMATION: The reference sequence is identical to\nCP084227.1.\nBacteria and source DNA available from Pol Nadal Jimenez, Institute\nof Infection, Veterinary and Ecological Sciences, University of\nLiverpool, Ic2 Liverpool Science Park, 146 Brownlow Hill,\nLiverpool, L3 5RF, UK.\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 Method :: Flye v. 2.8; Pilon v. 1.23\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 49.6x\nSequencing Technology :: Oxford Nanopore MinION; Illumina MiSeq\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 09/04/2022 11:51:30\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.2\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA;\n repeat_region\nGenes (total) :: 3,553\nCDSs (total) :: 3,453\nGenes (coding) :: 3,222\nCDSs (with protein) :: 3,222\nGenes (RNA) :: 100\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 70\nncRNAs :: 8\nPseudo Genes (total) :: 231\nCDSs (without protein) :: 231\nPseudo Genes (ambiguous residues) :: 0 of 231\nPseudo Genes (frameshifted) :: 136 of 231\nPseudo Genes (incomplete) :: 66 of 231\nPseudo Genes (internal stop) :: 64 of 231\nPseudo Genes (multiple problems) :: 33 of 231\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: similar to AA sequence:RefSeq:WP_015873870.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
Rpn family recombination-promoting nuclease/putative transposase
COORDINATES: protein motif:HMM:NF016255.2
COORDINATES: similar to AA sequence:RefSeq:WP_009309960.1
COORDINATES: similar to AA sequence:RefSeq:WP_006687041.1
MobC family replication-relaxation protein
COORDINATES: similar to AA sequence:RefSeq:WP_017346477.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_010845493.1
COORDINATES: similar to AA sequence:RefSeq:WP_020314981.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
frameshifted; 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: protein motif:HMM:NF040300.1
COORDINATES: similar to AA sequence:RefSeq:WP_001505436.1
COORDINATES: similar to AA sequence:RefSeq:WP_009635187.1
TrbM/KikA/MpfK family conjugal transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_004929670.1
COORDINATES: protein motif:HMM:NF016785.2
shufflon system plasmid conjugative transfer pilus tip adhesin PilV
COORDINATES: similar to AA sequence:RefSeq:WP_006869537.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_012987825.1
type II toxin-antitoxin system VapC family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_010891189.1
COORDINATES: protein motif:HMM:NF018642.2
GO:0016788 - hydrolase activity, acting on ester bonds [Evidence IEA]; GO:0043022 - ribosome binding [Evidence IEA]; GO:0003723 - RNA binding [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000412701.1
COORDINATES: similar to AA sequence:RefSeq:WP_011146158.1
COORDINATES: protein motif:HMM:NF013632.2
COORDINATES: similar to AA sequence:RefSeq:WP_015873682.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_015873680.1
COORDINATES: similar to AA sequence:RefSeq:WP_021141233.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_020308204.1
COORDINATES: similar to AA sequence:RefSeq:WP_017348369.1
COORDINATES: similar to AA sequence:RefSeq:WP_010400642.1
COORDINATES: protein motif:HMM:NF023291.2
COORDINATES: similar to AA sequence:RefSeq:WP_016809496.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001556584.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_005249500.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
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_014003226.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
type II toxin-antitoxin system RelB/DinJ family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_013521176.1
type II toxin-antitoxin system YafQ family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_009351668.1
COORDINATES: similar to AA sequence:RefSeq:WP_016257341.1
PBSX family phage terminase large subunit
COORDINATES: protein motif:HMM:NF012529.2
COORDINATES: protein motif:HMM:NF024258.2
GO:0016787 - hydrolase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_012987515.1
COORDINATES: similar to AA sequence:RefSeq:WP_010617320.1
COORDINATES: similar to AA sequence:RefSeq:WP_005918230.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873789.1
COORDINATES: similar to AA sequence:RefSeq:WP_003531811.1