Atlantibacter subterranea strain LH84-a plasmid pLH84-a-A, complete sequence.
Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Atlantibacter.
ESBL-producing Enterobacteriaceae from poultry
Submitted (05-JUL-2022) Institute for Food Safety and Hygiene, University of Zurich, Winterthurerstrasse 272, Zurich 8057, Switzerland
REFSEQ INFORMATION: The reference sequence is identical to\nCP100495.1.\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 :: Unicycler v. 0.5.0\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 100x, 100x\nSequencing Technology :: Illumina MiniSeq, Oxford Nanopore\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 07/22/2023 02:37:31\nAnnotation Pipeline :: NCBI Prokaryotic Genome\n Annotation Pipeline (PGAP)\nAnnotation Method :: Best-placed reference protein\n set; GeneMarkS-2+\nAnnotation Software revision :: 6.5\nFeatures Annotated :: Gene; CDS; rRNA; tRNA; ncRNA\nGenes (total) :: 4,551\nCDSs (total) :: 4,436\nGenes (coding) :: 4,382\nCDSs (with protein) :: 4,382\nGenes (RNA) :: 115\nrRNAs :: 8, 7, 7 (5S, 16S, 23S)\ncomplete rRNAs :: 8, 7, 7 (5S, 16S, 23S)\ntRNAs :: 84\nncRNAs :: 9\nPseudo Genes (total) :: 54\nCDSs (without protein) :: 54\nPseudo Genes (ambiguous residues) :: 0 of 54\nPseudo Genes (frameshifted) :: 22 of 54\nPseudo Genes (incomplete) :: 38 of 54\nPseudo Genes (internal stop) :: 9 of 54\nPseudo Genes (multiple problems) :: 12 of 54\nCRISPR Arrays :: 1\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
Institute for Food Safety and Hygiene, University of Zurich
COORDINATES: similar to AA sequence:RefSeq:WP_001549892.1
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_001549893.1
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_000516401.1
COORDINATES: similar to AA sequence:RefSeq:WP_001371664.1
COORDINATES: similar to AA sequence:RefSeq:WP_000469598.1
COORDINATES: similar to AA sequence:RefSeq:WP_001043731.1
COORDINATES: similar to AA sequence:RefSeq:WP_000202950.1
COORDINATES: similar to AA sequence:RefSeq:WP_001074369.1
COORDINATES: similar to AA sequence:RefSeq:WP_001348704.1
GO:0003887 - DNA-directed DNA polymerase activity [Evidence IEA]
GO:0006270 - DNA replication initiation [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000127484.1
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_001025391.1
COORDINATES: similar to AA sequence:RefSeq:WP_006122499.1
COORDINATES: similar to AA sequence:RefSeq:WP_001549906.1
COORDINATES: similar to AA sequence:RefSeq:WP_001549907.1
COORDINATES: similar to AA sequence:RefSeq:WP_000008707.1
COORDINATES: similar to AA sequence:RefSeq:WP_001549908.1
COORDINATES: similar to AA sequence:RefSeq:WP_000004083.1
COORDINATES: similar to AA sequence:RefSeq:WP_001549910.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_000757693.1
COORDINATES: similar to AA sequence:RefSeq:WP_001549912.1
COORDINATES: similar to AA sequence:RefSeq:WP_000455437.1
GO:0006355 - regulation of DNA-templated transcription [Evidence IEA]
transcription termination/antitermination NusG family protein
COORDINATES: similar to AA sequence:RefSeq:WP_001549915.1
lytic transglycosylase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_000916156.1
COORDINATES: similar to AA sequence:RefSeq:WP_016247738.1
VirB3 family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_001549917.1
COORDINATES: similar to AA sequence:RefSeq:WP_000759841.1
COORDINATES: similar to AA sequence:RefSeq:WP_001549919.1
COORDINATES: similar to AA sequence:RefSeq:WP_004199085.1
COORDINATES: similar to AA sequence:RefSeq:WP_000783379.1
TrbG/VirB9 family P-type conjugative transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_001295060.1
VirB10/TraB/TrbI family type IV secretion system protein
COORDINATES: similar to AA sequence:RefSeq:WP_000629109.1
COORDINATES: similar to AA sequence:RefSeq:WP_001549925.1
GO:0043684 - type IV secretion system complex [Evidence IEA]
GO:0044097 - secretion by the type IV secretion system [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_000053816.1
type IV secretory system conjugative DNA transfer family protein
COORDINATES: similar to AA sequence:RefSeq:WP_000738524.1
cag pathogenicity island Cag12 family protein
COORDINATES: similar to AA sequence:RefSeq:WP_000754496.1
TrbM/KikA/MpfK family conjugal transfer protein
COORDINATES: similar to AA sequence:RefSeq:WP_004208538.1
COORDINATES: similar to AA sequence:RefSeq:WP_001215543.1
COORDINATES: similar to AA sequence:RefSeq:WP_000517490.1
COORDINATES: similar to AA sequence:RefSeq:WP_001549937.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0003917 - DNA topoisomerase type I (single strand cut, ATP-independent) activity [Evidence IEA]
GO:0006265 - DNA topological change [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_001549938.1
H-NS family nucleoid-associated regulatory protein
COORDINATES: protein motif:HMM:NF015639.2
COORDINATES: similar to AA sequence:RefSeq:WP_086558238.1
GO:0004803 - transposase activity [Evidence IEA]
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: nucleotide motif:Rfam:14.4:RF01497
AL1L pseudoknot; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_000447023.1
COORDINATES: similar to AA sequence:RefSeq:WP_001282653.1
IS21-like element ISSso4 family helper ATPase IstB
COORDINATES: similar to AA sequence:RefSeq:WP_000136657.1
COORDINATES: similar to AA sequence:RefSeq:WP_000196235.1
COORDINATES: similar to AA sequence:RefSeq:WP_000510385.1
COORDINATES: similar to AA sequence:RefSeq:WP_000557557.1
COORDINATES: similar to AA sequence:RefSeq:WP_001093608.1
COORDINATES: similar to AA sequence:RefSeq:WP_000609149.1
COORDINATES: similar to AA sequence:RefSeq:WP_001493761.1
ISKra4-like element ISKpn19 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_001493762.1
COORDINATES: similar to AA sequence:RefSeq:WP_001493763.1
COORDINATES: similar to AA sequence:RefSeq:WP_015060658.1
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_017412822.1
COORDINATES: similar to AA sequence:RefSeq:WP_001516695.1
quinolone resistance pentapeptide repeat protein QnrS1
COORDINATES: similar to AA sequence:RefSeq:YP_005221000.1
IS6-like element IS26 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_001549890.1
helix-turn-helix domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:YP_005226821.1
GO:0003700 - DNA-binding transcription factor activity [Evidence IEA]
DeoR/GlpR family DNA-binding transcription regulator
COORDINATES: similar to AA sequence:RefSeq:WP_001620095.1
extended-spectrum class A beta-lactamase SHV-12