Arsenophonus apicola strain ArsBeeUS plasmid pArsBee4, 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\nCP084226.1.\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: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: similar to AA sequence:RefSeq:WP_019923820.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF037421.2
COORDINATES: similar to AA sequence:RefSeq:WP_007247727.1
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_001749339.1
plasmid mobilization relaxosome protein MobC
COORDINATES: similar to AA sequence:RefSeq:WP_020313368.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003916 - DNA topoisomerase activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
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_004247964.1
COORDINATES: similar to AA sequence:RefSeq:WP_004247966.1
COORDINATES: similar to AA sequence:RefSeq:WP_016232708.1
incomplete; partial in the middle of a contig; missing N-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005785501.1
COORDINATES: similar to AA sequence:RefSeq:WP_012126733.1
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_008314477.1
COORDINATES: similar to AA sequence:RefSeq:WP_006661035.1
COORDINATES: similar to AA sequence:RefSeq:WP_008910114.1
GO:0033573 - high-affinity iron permease complex [Evidence IEA]; GO:0016020 - membrane [Evidence IEA]
GO:0005381 - iron ion transmembrane transporter activity [Evidence IEA]
GO:0034755 - iron ion transmembrane transport [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_008910113.1
COORDINATES: similar to AA sequence:RefSeq:WP_008910112.1
GO:0020037 - heme binding [Evidence IEA]; GO:0004601 - peroxidase activity [Evidence IEA]
GO:0033212 - iron import into cell [Evidence IEA]
iron uptake transporter deferrochelatase/peroxidase subunit
COORDINATES: similar to AA sequence:RefSeq:WP_076612135.1
frameshifted; 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_016713586.1
frameshifted; internal stop; 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.
reverse transcriptase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005720092.1
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:NP_415949.3
COORDINATES: similar to AA sequence:RefSeq:WP_007969325.1
COORDINATES: similar to AA sequence:RefSeq:WP_011082269.1
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:NF013676.2
COORDINATES: similar to AA sequence:RefSeq:WP_004144477.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_020308204.1
COORDINATES: similar to AA sequence:RefSeq:WP_021141233.1
COORDINATES: protein motif:HMM:NF019984.2
COORDINATES: protein motif:HMM:TIGR04416.1
GO:0003964 - RNA-directed DNA polymerase activity [Evidence IEA]
GO:0000373 - Group II intron splicing [Evidence IEA]
group II intron reverse transcriptase/maturase
programmed frameshift; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013535.2
COORDINATES: similar to AA sequence:RefSeq:WP_001556584.1
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: protein motif:HMM:NF020037.2
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_011409936.1
COORDINATES: protein motif:HMM:NF012422.2
COORDINATES: similar to AA sequence:RefSeq:WP_006118548.1
COORDINATES: similar to AA sequence:RefSeq:WP_006704154.1
COORDINATES: similar to AA sequence:RefSeq:WP_010865085.1
COORDINATES: similar to AA sequence:RefSeq:WP_015981317.1
Rpn family recombination-promoting nuclease/putative transposase
COORDINATES: protein motif:HMM:NF016255.2