Arsenophonus apicola strain ArsBeeUS plasmid pArsBee1, 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\nCP084223.1.\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_016809496.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_001556584.1
GO:0004803 - transposase activity [Evidence IEA]
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF020137.2
GO:0005615 - extracellular space [Evidence IEA]
GO:0005509 - calcium ion binding [Evidence IEA]
M10 family metallopeptidase C-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_008182253.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_011345576.1
frameshifted; incomplete; partial in the middle of a contig; missing N-terminus; 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:NF012774.2
COORDINATES: similar to AA sequence:RefSeq:WP_004239652.1
GO:0003684 - damaged DNA binding [Evidence IEA]
translesion error-prone DNA polymerase V subunit UmuC
COORDINATES: similar to AA sequence:RefSeq:WP_000165970.1
Rop family plasmid primer RNA-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_005759576.1
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_001419705.1
COORDINATES: similar to AA sequence:RefSeq:WP_010865085.1
COORDINATES: similar to AA sequence:RefSeq:WP_006708696.1
COORDINATES: similar to AA sequence:RefSeq:WP_017709574.1
COORDINATES: similar to AA sequence:RefSeq:WP_005734862.1
COORDINATES: protein motif:HMM:NF014316.2
COORDINATES: similar to AA sequence:RefSeq:WP_003935408.1
COORDINATES: similar to AA sequence:RefSeq:WP_001722340.1
COORDINATES: similar to AA sequence:RefSeq:WP_006954077.1
COORDINATES: similar to AA sequence:RefSeq:WP_014657458.1
COORDINATES: similar to AA sequence:RefSeq:WP_000523346.1
COORDINATES: protein motif:HMM:NF020569.2
GO:0016788 - hydrolase activity, acting on ester bonds [Evidence IEA]; GO:0043022 - ribosome binding [Evidence IEA]; GO:0003723 - RNA binding [Evidence IEA]
COORDINATES: protein motif:HMM:NF018642.2
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: similar to AA sequence:RefSeq:WP_002212004.1
COORDINATES: similar to AA sequence:RefSeq:WP_015377597.1
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: protein motif:HMM:NF012694.2
type II secretion system F family protein
COORDINATES: similar to AA sequence:RefSeq:WP_001595120.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_020317119.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_015873778.1
COORDINATES: protein motif:HMM:TIGR03021.1
GO:0009297 - pilus assembly [Evidence IEA]
COORDINATES: protein motif:HMM:NF018562.2
COORDINATES: similar to AA sequence:RefSeq:WP_015873775.1
GO:0019867 - outer membrane [Evidence IEA]
GO:0009297 - pilus assembly [Evidence IEA]; GO:0009306 - protein secretion [Evidence IEA]
PilN family type IVB pilus formation outer membrane protein
COORDINATES: similar to AA sequence:RefSeq:WP_006660993.1
COORDINATES: protein motif:HMM:NF013618.2
COORDINATES: similar to AA sequence:RefSeq:WP_019674184.1
COORDINATES: similar to AA sequence:RefSeq:WP_001041623.1
COORDINATES: similar to AA sequence:RefSeq:WP_006704154.1
COORDINATES: similar to AA sequence:RefSeq:WP_015873814.1
COORDINATES: protein motif:HMM:NF020835.2
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_009637177.1
PAS and helix-turn-helix domain-containing protein
COORDINATES: protein motif:HMM:NF017337.2
COORDINATES: protein motif:HMM:NF017152.2
type IV conjugative transfer system protein TraE
COORDINATES: protein motif:HMM:NF015688.2
COORDINATES: protein motif:HMM:NF022580.2
COORDINATES: protein motif:HMM:NF040179.1
COORDINATES: protein motif:HMM:NF021213.2
COORDINATES: similar to AA sequence:RefSeq:WP_016529742.1
conjugal transfer pilus assembly protein TraU
COORDINATES: similar to AA sequence:RefSeq:WP_020802381.1
type-F conjugative transfer system pilin assembly protein TrbC
COORDINATES: protein motif:HMM:NF018666.2
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_020802380.1
type-F conjugative transfer system pilin assembly protein TraF
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: similar to AA sequence:RefSeq:WP_016236308.1
COORDINATES: similar to AA sequence:RefSeq:WP_000850426.1
type IV secretion system DNA-binding domain-containing protein
COORDINATES: protein motif:HMM:NF014581.2
COORDINATES: protein motif:HMM:TIGR02686.1
GO:0004386 - helicase activity [Evidence IEA]
GO:0006259 - DNA metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000034825.1
COORDINATES: similar to AA sequence:RefSeq:WP_004705335.1
phosphate-starvation-inducible protein PsiE
COORDINATES: similar to AA sequence:RefSeq:WP_004963009.1
COORDINATES: similar to AA sequence:RefSeq:WP_011279233.1
COORDINATES: protein motif:HMM:NF020704.2
COORDINATES: protein motif:HMM:NF017542.2