Enterococcus lactis strain CX 2-6_2 plasmid pXC, complete sequence.
Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae; Enterococcus.
A pan-genome analysis of Enterococcus faecium CX 2-6 genomes reveals gene clusters in response to heavy metal stress
Submitted (28-JUN-2021) Institute of Applied Microbiology, Jiangxi Agricultural University, No. 1101 Zhimin Avenue, Nanchang 330045, China
REFSEQ INFORMATION: The reference sequence is identical to\nCP079881.1.\nBacteria and source DNA available from Institute of Applied\nMicrobiology, Jiangxi Agricultural University.\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 :: HGAP v. JUN-2019\nGenome Representation :: Full\nExpected Final Version :: Yes\nGenome Coverage :: 90.0x\nSequencing Technology :: PacBio\n##Genome-Assembly-Data-END##\n\n##Genome-Annotation-Data-START##\nAnnotation Provider :: NCBI RefSeq\nAnnotation Date :: 03/25/2023 05:39:37\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) :: 2,669\nCDSs (total) :: 2,580\nGenes (coding) :: 2,491\nCDSs (with protein) :: 2,491\nGenes (RNA) :: 89\nrRNAs :: 6, 6, 6 (5S, 16S, 23S)\ncomplete rRNAs :: 6, 6, 6 (5S, 16S, 23S)\ntRNAs :: 67\nncRNAs :: 4\nPseudo Genes (total) :: 89\nCDSs (without protein) :: 89\nPseudo Genes (ambiguous residues) :: 0 of 89\nPseudo Genes (frameshifted) :: 30 of 89\nPseudo Genes (incomplete) :: 36 of 89\nPseudo Genes (internal stop) :: 35 of 89\nPseudo Genes (multiple problems) :: 10 of 89\n##Genome-Annotation-Data-END##\nCOMPLETENESS: full length.
COORDINATES: protein motif:HMM:NF021111.2
GO:0003677 - DNA binding [Evidence IEA]; GO:0009036 - type II site-specific deoxyribonuclease activity [Evidence IEA]
GO:0009307 - DNA restriction-modification system [Evidence IEA]
Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_002347711.1
GO:0004803 - transposase activity [Evidence IEA]
COORDINATES: ab initio prediction:GeneMarkS-2+
Derived by automated computational analysis using gene prediction method: GeneMarkS-2+.
COORDINATES: protein motif:HMM:NF012311.2
GO:0008236 - serine-type peptidase activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002348804.1
COORDINATES: similar to AA sequence:RefSeq:WP_002335394.1
COORDINATES: similar to AA sequence:RefSeq:WP_002334620.1
COORDINATES: similar to AA sequence:RefSeq:WP_002292679.1
type II toxin-antitoxin system mRNA interferase toxin, RelE/StbE family
COORDINATES: similar to AA sequence:RefSeq:WP_005877489.1
COORDINATES: similar to AA sequence:RefSeq:WP_002305108.1
frameshifted; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_002344902.1
type II toxin-antitoxin system Phd/YefM family antitoxin
COORDINATES: similar to AA sequence:RefSeq:WP_076611882.1
IS982-like element ISEfm1 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_016618833.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0000150 - DNA strand exchange activity [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]
internal stop; 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_016627933.1
type 1 glutamine amidotransferase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_053338758.1
frameshifted; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_015083012.1
COORDINATES: similar to AA sequence:RefSeq:WP_015639662.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0004519 - endonuclease activity [Evidence IEA]
GO:0006304 - DNA modification [Evidence IEA]
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_003551875.1
COORDINATES: similar to AA sequence:RefSeq:WP_002335311.1
COORDINATES: similar to AA sequence:RefSeq:WP_002314395.1
COORDINATES: similar to AA sequence:RefSeq:WP_064305258.1
IS6-like element IS1216 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_002318298.1
type II toxin-antitoxin system RelE/ParE family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_002318299.1
COORDINATES: similar to AA sequence:RefSeq:WP_002290398.1
COORDINATES: similar to AA sequence:RefSeq:WP_002339775.1
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_002310953.1
COORDINATES: similar to AA sequence:RefSeq:WP_002310954.1
type IV conjugative transfer system protein TraE
COORDINATES: similar to AA sequence:RefSeq:WP_002325562.1
COORDINATES: similar to AA sequence:RefSeq:WP_002311523.1
COORDINATES: similar to AA sequence:RefSeq:WP_002311524.1
COORDINATES: similar to AA sequence:RefSeq:WP_002322851.1
COORDINATES: similar to AA sequence:RefSeq:WP_002295671.1
COORDINATES: similar to AA sequence:RefSeq:WP_002332682.1
SpaA isopeptide-forming pilin-related protein
COORDINATES: similar to AA sequence:RefSeq:WP_002349627.1
COORDINATES: similar to AA sequence:RefSeq:WP_016177596.1
pilin N-terminal domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_000221326.1
IS30-like element IS6770 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_002314417.1
COORDINATES: similar to AA sequence:RefSeq:WP_002307536.1
COORDINATES: similar to AA sequence:RefSeq:WP_002295649.1
GO:0004040 - amidase activity [Evidence IEA]
glucosaminidase domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002326164.1
COORDINATES: similar to AA sequence:RefSeq:WP_002295645.1
COORDINATES: similar to AA sequence:RefSeq:WP_010731508.1
COORDINATES: similar to AA sequence:RefSeq:WP_002332286.1
COORDINATES: similar to AA sequence:RefSeq:WP_002342432.1
GO:0042742 - defense response to bacterium [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002299246.1
COORDINATES: similar to AA sequence:RefSeq:WP_002364712.1
COORDINATES: similar to AA sequence:RefSeq:WP_002295641.1
COORDINATES: similar to AA sequence:RefSeq:WP_002316069.1
COORDINATES: similar to AA sequence:RefSeq:WP_002302840.1
COORDINATES: similar to AA sequence:RefSeq:WP_002347694.1
ArdC-like ssDNA-binding domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_014401506.1
COORDINATES: similar to AA sequence:RefSeq:WP_002369673.1
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_002344867.1
COORDINATES: similar to AA sequence:RefSeq:WP_002330586.1
type IV toxin-antitoxin system AbiEi family antitoxin domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002293531.1
nucleotidyl transferase AbiEii/AbiGii toxin family protein
GO:0003697 - single-stranded DNA binding [Evidence IEA]
GO:0006310 - DNA recombination [Evidence IEA]; GO:0006281 - DNA repair [Evidence IEA]; GO:0006260 - DNA replication [Evidence IEA]; GO:0006351 - DNA-templated transcription [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002339774.1
COORDINATES: similar to AA sequence:RefSeq:WP_016853414.1
COORDINATES: similar to AA sequence:RefSeq:WP_002314430.1
COORDINATES: similar to AA sequence:RefSeq:WP_016922517.1
COORDINATES: similar to AA sequence:RefSeq:WP_002293546.1
COORDINATES: similar to AA sequence:RefSeq:WP_002311003.1
COORDINATES: similar to AA sequence:RefSeq:WP_002311004.1
COORDINATES: protein motif:HMM:NF013850.2
GO:0005576 - extracellular region [Evidence IEA]
leucocin A/sakacin P family class II bacteriocin
COORDINATES: similar to AA sequence:RefSeq:WP_016177651.1
COORDINATES: similar to AA sequence:RefSeq:WP_002287843.1
internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: protein motif:HMM:NF013235.2
COORDINATES: similar to AA sequence:RefSeq:WP_002292473.1
COORDINATES: similar to AA sequence:RefSeq:WP_002322958.1
COORDINATES: similar to AA sequence:RefSeq:WP_012477736.1
incomplete; partial in the middle of a contig; missing C-terminus; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: nucleotide motif:Rfam:14.4:RF00230
T-box leader; Derived by automated computational analysis using gene prediction method: cmsearch.
COORDINATES: similar to AA sequence:RefSeq:WP_010744711.1
MetQ/NlpA family ABC transporter substrate-binding protein
COORDINATES: similar to AA sequence:RefSeq:WP_002334638.1
GO:0033744 - L-methionine:thioredoxin-disulfide S-oxidoreductase activity [Evidence IEA]; GO:0008113 - peptide-methionine (S)-S-oxide reductase activity [Evidence IEA]
GO:0030091 - protein repair [Evidence IEA]; GO:0006979 - response to oxidative stress [Evidence IEA]
peptide-methionine (S)-S-oxide reductase MsrA
COORDINATES: similar to AA sequence:RefSeq:WP_016629718.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611768.1
programmed frameshift; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_002293183.1
enterocin L50 family leaderless bacteriocin
COORDINATES: similar to AA sequence:RefSeq:WP_002293184.1
COORDINATES: similar to AA sequence:RefSeq:WP_002329885.1
COORDINATES: similar to AA sequence:RefSeq:WP_002293186.1
COORDINATES: similar to AA sequence:RefSeq:WP_002293187.1
COORDINATES: similar to AA sequence:RefSeq:WP_002293188.1
COORDINATES: similar to AA sequence:RefSeq:WP_002293189.1
COORDINATES: similar to AA sequence:RefSeq:WP_002293190.1
HlyD family efflux transporter periplasmic adaptor subunit
COORDINATES: similar to AA sequence:RefSeq:WP_002368629.1
COORDINATES: similar to AA sequence:RefSeq:WP_002293193.1
COORDINATES: similar to AA sequence:RefSeq:WP_002344659.1
COORDINATES: similar to AA sequence:RefSeq:WP_002308079.1
COORDINATES: similar to AA sequence:RefSeq:WP_003728509.1
helix-turn-helix transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_005470367.1
ATP-dependent Clp protease ATP-binding subunit
COORDINATES: similar to AA sequence:RefSeq:WP_076611172.1
COORDINATES: similar to AA sequence:RefSeq:WP_002362392.1
COORDINATES: similar to AA sequence:RefSeq:WP_002334568.1
COORDINATES: similar to AA sequence:RefSeq:WP_002324322.1
IS256-like element ISEfm2 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_002321532.1
COORDINATES: similar to AA sequence:RefSeq:WP_002322258.1
COORDINATES: similar to AA sequence:RefSeq:WP_002291922.1
programmed frameshift; internal stop; Derived by automated computational analysis using gene prediction method: Protein Homology.
COORDINATES: similar to AA sequence:RefSeq:WP_002329895.1
ATP-binding cassette domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_005880299.1
COORDINATES: similar to AA sequence:RefSeq:WP_002341371.1
COORDINATES: similar to AA sequence:RefSeq:WP_010749154.1
COORDINATES: similar to AA sequence:RefSeq:WP_002318452.1
iron export ABC transporter permease subunit FetB
COORDINATES: similar to AA sequence:RefSeq:WP_002376288.1
COORDINATES: similar to AA sequence:RefSeq:WP_002338071.1
COORDINATES: similar to AA sequence:RefSeq:WP_002307501.1
GO:0016301 - kinase activity [Evidence IEA]
type II toxin-antitoxin system death-on-curing family toxin
COORDINATES: similar to AA sequence:RefSeq:WP_002290351.1
COORDINATES: similar to AA sequence:RefSeq:WP_016177643.1
GO:0015074 - DNA integration [Evidence IEA]; GO:0006310 - DNA recombination [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002342363.1
COORDINATES: similar to AA sequence:RefSeq:WP_016623907.1
COORDINATES: protein motif:HMM:NF013752.2
COORDINATES: similar to AA sequence:RefSeq:WP_002290364.1
GO:0004645 - 1,4-alpha-oligoglucan phosphorylase activity [Evidence IEA]
GO:0005975 - carbohydrate metabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002342361.1
GO:0003824 - catalytic activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002338079.1
COORDINATES: similar to AA sequence:RefSeq:WP_000711263.1
COORDINATES: similar to AA sequence:RefSeq:WP_018363968.1
COORDINATES: similar to AA sequence:RefSeq:WP_002343070.1
COORDINATES: similar to AA sequence:RefSeq:WP_002324535.1
COORDINATES: similar to AA sequence:RefSeq:WP_002405323.1
COORDINATES: similar to AA sequence:RefSeq:WP_002338086.1
COORDINATES: protein motif:HMM:NF024808.2
COORDINATES: protein motif:HMM:NF013697.2
COORDINATES: protein motif:HMM:NF024770.2
substrate-binding domain-containing protein
COORDINATES: protein motif:HMM:NF012742.2
LacI family DNA-binding transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_016634498.1
COORDINATES: protein motif:HMM:NF012798.2
COORDINATES: similar to AA sequence:RefSeq:WP_002318477.1
IS6-like element ISS1N family transposase
COORDINATES: protein motif:HMM:NF013753.2
COORDINATES: similar to AA sequence:RefSeq:WP_002351732.1
COORDINATES: similar to AA sequence:RefSeq:WP_002307659.1
COORDINATES: similar to AA sequence:RefSeq:WP_002294791.1
HAMP domain-containing sensor histidine kinase
COORDINATES: similar to AA sequence:RefSeq:WP_002339652.1
COORDINATES: similar to AA sequence:RefSeq:WP_002344896.1
COORDINATES: similar to AA sequence:RefSeq:WP_002339788.1
COORDINATES: similar to AA sequence:RefSeq:WP_002338028.1
GO:0019812 - type I site-specific deoxyribonuclease complex [Evidence IEA]
GO:0009035 - type I site-specific deoxyribonuclease activity [Evidence IEA]
HsdR family type I site-specific deoxyribonuclease
COORDINATES: protein motif:HMM:NF013579.2
COORDINATES: similar to AA sequence:RefSeq:WP_002338026.1
GO:0003677 - DNA binding [Evidence IEA]; GO:0008170 - N-methyltransferase activity [Evidence IEA]
GO:0006306 - DNA methylation [Evidence IEA]
type I restriction-modification system subunit M
COORDINATES: similar to AA sequence:RefSeq:WP_002405176.1
COORDINATES: similar to AA sequence:RefSeq:WP_016627749.1
COORDINATES: similar to AA sequence:RefSeq:WP_000997693.1
IS256-like element ISLgar5 family transposase
COORDINATES: similar to AA sequence:RefSeq:WP_015081805.1
COORDINATES: similar to AA sequence:RefSeq:WP_007208410.1
COORDINATES: similar to AA sequence:RefSeq:WP_076611665.1
COORDINATES: similar to AA sequence:RefSeq:WP_007209263.1
COORDINATES: similar to AA sequence:RefSeq:WP_002316685.1
metalloregulator ArsR/SmtB family transcription factor
COORDINATES: similar to AA sequence:RefSeq:WP_002342451.1
cation diffusion facilitator family transporter
COORDINATES: similar to AA sequence:RefSeq:WP_002320189.1
CadD family cadmium resistance transporter
COORDINATES: similar to AA sequence:RefSeq:WP_000754864.1
COORDINATES: similar to AA sequence:RefSeq:WP_002292162.1
COORDINATES: similar to AA sequence:RefSeq:WP_003106687.1
heavy-metal-associated domain-containing protein
COORDINATES: similar to AA sequence:RefSeq:WP_002371076.1
GO:0008961 - phosphatidylglycerol-prolipoprotein diacylglyceryl transferase activity [Evidence IEA]
GO:0009249 - protein lipoylation [Evidence IEA]
prolipoprotein diacylglyceryl transferase
COORDINATES: similar to AA sequence:RefSeq:WP_002293763.1
COORDINATES: similar to AA sequence:RefSeq:WP_011476586.1
Crp/Fnr family transcriptional regulator
COORDINATES: similar to AA sequence:RefSeq:WP_003706982.1
DNA starvation/stationary phase protection protein
COORDINATES: protein motif:HMM:NF022641.2
COORDINATES: similar to AA sequence:RefSeq:WP_002291321.1
COORDINATES: similar to AA sequence:RefSeq:WP_002342391.1
endonuclease/exonuclease/phosphatase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_002363316.1
GO:0015144 - carbohydrate transmembrane transporter activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002319549.1
COORDINATES: similar to AA sequence:RefSeq:WP_019722730.1
GO:0008801 - beta-phosphoglucomutase activity [Evidence IEA]
GO:0046352 - disaccharide catabolic process [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_016177275.1
COORDINATES: similar to AA sequence:RefSeq:WP_016628946.1
GO:0016810 - hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds [Evidence IEA]
polysaccharide deacetylase family protein
COORDINATES: similar to AA sequence:RefSeq:WP_002343693.1
GO:0004527 - exonuclease activity [Evidence IEA]
COORDINATES: similar to AA sequence:RefSeq:WP_002342384.1
COORDINATES: similar to AA sequence:RefSeq:WP_002331328.1
COORDINATES: similar to AA sequence:RefSeq:WP_000136908.1
COORDINATES: similar to AA sequence:RefSeq:WP_002334404.1
COORDINATES: similar to AA sequence:RefSeq:WP_016385736.1
COORDINATES: similar to AA sequence:RefSeq:WP_002343106.1
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]