LOCUS       NZ_CP035652             4316 bp    DNA     circular CON 17-JUN-2024
DEFINITION  Enterococcus faecium strain UAMSEF_08 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP035652
VERSION     NZ_CP035652.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN10863491
            Assembly: GCF_005886655.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4316)
  AUTHORS   Udaondo,Z., Abram,K., Kothari,A. and Jun,S.R.
  TITLE     Top-Down Genomic Surveillance Approach To Investigate the Genomic
            Epidemiology and Antibiotic Resistance Patterns of Enterococcus
            faecium Detected in Cancer Patients in Arkansas
  JOURNAL   Microbiol Spectr 11 (3), e0490122 (2023)
   PUBMED   36995227
REFERENCE   2  (bases 1 to 4316)
  AUTHORS   Jenjaroenpun,P.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-FEB-2019) Biomedical Informatics, University of
            Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR
            72205, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: JAN-2019
            Assembly Method                   :: Unicycler v. 0.4.4
            Assembly Name                     :: UAMS_Efae_0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 483.0x
            Sequencing Technology :: Oxford Nanopore MiniION; Illumina NextSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_005886655.1-RS_2024_06_17
            Annotation Date                   :: 06/17/2024 10:52:15
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 3,114
            CDSs (total)                      :: 3,023
            Genes (coding)                    :: 2,796
            CDSs (with protein)               :: 2,796
            Genes (RNA)                       :: 91
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 69
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 227
            CDSs (without protein)            :: 227
            Pseudo Genes (ambiguous residues) :: 0 of 227
            Pseudo Genes (frameshifted)       :: 133 of 227
            Pseudo Genes (incomplete)         :: 91 of 227
            Pseudo Genes (internal stop)      :: 43 of 227
            Pseudo Genes (multiple problems)  :: 33 of 227
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP035652.1.
            Bacteria and source DNA available from Tip's lab.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..4316
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="UAMSEF_08"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="unnamed4"
                     /geo_loc_name="USA:Arkansas"
                     /collection_date="2018-07-07"
     gene            join(4095..4316,1..1185)
                     /locus_tag="EWM54_RS00270"
                     /old_locus_tag="EWM54_00270"
     CDS             join(4095..4316,1..1185)
                     /locus_tag="EWM54_RS00270"
                     /old_locus_tag="EWM54_00270"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173818.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid recombination protein"
                     /protein_id="WP_060800944.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDSQKINDWHKHIDFTKSDENI
                     YLEQTNIREKYEELFGEAVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGTL
                     DDFRTTRDDGSSTGISEQQAEQNRVIANKILVEYFKEFKERNPSLSVYNAVIHNDEVSP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALQQQGLRADKENGRVIWNNFRNQEVESIERLMA
                     DFGWERELVGTNKIKDVHEYKEIMSEISELRQTAVKERESVSDELGYISRQREENEREK
                     ALVASERAKIEEEKKNMLNVKKEMAVIFQKDIVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKKAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQHK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     gene            1785..2774
                     /locus_tag="EWM54_RS00275"
                     /old_locus_tag="EWM54_00275"
     CDS             1785..2774
                     /locus_tag="EWM54_RS00275"
                     /old_locus_tag="EWM54_00275"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002349057.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_002304903.1"
                     /translation="MKKKKQDLINGTFREKKKNLKKVVAFSDNRISPKMRELMTGCGSY
                     LEFIATIDKEKKKLVQAHFCKNRFCPLCAWRKARKDSMMLSIMMQAIAEEKQYQFIFMT
                     LTTPNVKAECLNDEIDLFNHALKKMFMRKRVKTSIKGYVRKLEITYNKKRNDYNPHFHL
                     ILAVNKSYFTDKDYYIKQSEWLDLWREVTGKTGINPDGTDEITQLDIRKVKGFQQEKAV
                     QEVAKYSAKDFELTESQEVFDTFYHAMKGRQLITFNGVFKEYKKKYESGDLDRYKKKDE
                     NEYFWFLTASWMRKESKYAVDYREMSADERNYFSGMYVDEKSVEGENE"
                     /name="protein rep"
     gene            2771..3190
                     /locus_tag="EWM54_RS00280"
                     /old_locus_tag="EWM54_00280"
     CDS             2771..3190
                     /locus_tag="EWM54_RS00280"
                     /old_locus_tag="EWM54_00280"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002351943.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002305964.1"
                     /translation="MTDSTDKMTIKALADELGITKNTVRNYLVKAGYDLARYKKNGIIL
                     LDKELIGVARSIYRSKGGQLTGHLPVNSTGSDFPLEKENEFLRDQLAEKDKHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     gene            3169..3507
                     /locus_tag="EWM54_RS00285"
                     /old_locus_tag="EWM54_00285"
     CDS             3169..3507
                     /locus_tag="EWM54_RS00285"
                     /old_locus_tag="EWM54_00285"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002321903.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002305963.1"
                     /translation="MVAILEVRCDMDKIDLREETVNRIEVMYERLADYLNLSDEDNYSE
                     MLERMMDVLNSVINADLAKSSVLTNEFVHKHLAQTTDEAEKEFWLKLMSHIMQLNQISV
                     INSKEKGM"
                     /name="hypothetical protein"
     gene            3511..3873
                     /locus_tag="EWM54_RS00290"
                     /old_locus_tag="EWM54_00290"
     CDS             3511..3873
                     /locus_tag="EWM54_RS00290"
                     /old_locus_tag="EWM54_00290"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173819.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_130587602.1"
                     /translation="MGMTLADIKVQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFESFADFERWLSSISDDQQHEKSVDNEWLADEKSAPSERDYPNEYDGLLGVMPSKKSQ
                     MNESKFMSIFNDVNLR"
                     /name="hypothetical protein"
     Typing          2..1182
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.97"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gatagaaaaa tcgaggacta tttagcaaag gttcgcaagg ataaaaaatt ggaaccacag
       61 cgagaattta tcgtgcaaat tggtactctt gatgattttc gtactactcg tgatgatggt
      121 tcttctactg gcatatcgga acaacaagca gaacaaaatc gagtgattgc caacaaaatt
      181 ttagttgagt atttcaaaga atttaaagaa cggaatccta gtttatccgt ctacaatgct
      241 gttattcata atgacgaagt aagtccgcac ctgcatttga atattgttcc tgttgctgaa
      301 gggtataaac ggggtgttca aaagcaacca agttttaaca aagccttgca acagcagggt
      361 ttacgagcag ataaagagaa tggtcgagtg atttggaata attttaggaa tcaggaagtt
      421 gagtcaattg aacgtttgat ggcagatttt ggttgggagc gtgagttagt cggtactaac
      481 aaaatcaaag atgttcacga atataaagaa atcatgagcg agatttcaga attgcgtcaa
      541 acggccgtaa aagagcgtga gagcgtttct gatgagttgg ggtatatttc taggcaaaga
      601 gaagaaaacg agcgagaaaa ggctctggtg gcttctgaga gagcaaagat tgaagaagag
      661 aagaaaaata tgctgaatgt aaaaaaagag atggcggtca ttttccaaaa agatattgtt
      721 cctttagaaa gtttcaagag gcttcctgat ggttcgtatc atttatctgg gaatgatttt
      781 gttgatttgt atcaacgagc tacgagagca acaaatgcca agagaaatgc tgataacatg
      841 agtgagcaat atttacagat gcttgagcaa aatacagaat taaatgagta tgtagctaca
      901 ttggaagaag agcgtcattt gtctggtaga aaacaattag cagatttaca agtggaaaat
      961 aaaaagctga aagaagaaaa tcgctcttta cgccagcgtt tagagcgatt aaaaaaagca
     1021 tttcaaaaat cgatcactcg tttgtctatc cgttttggtc ttgcagaaaa ggatatgggg
     1081 ctttctgagg aattagaagt attagagcag gagaaaacct tattttatcg tcaaaacgtc
     1141 tcacagcata aattagagcg ttctgaagat gagatcgagt ggtagttacg atgtgcagtc
     1201 aacggtaccg gaggcggtct gtgccgagga taaggagttg acggctaaac cactagccta
     1261 ttaagctgac atttgctaaa aaatggcaag tccatttttt ggccaaccta gcgttagcga
     1321 aagtttgggg gcgccctttt caaagggagc ggttttattt ttgcatgact aagaatgagt
     1381 gggaaaaact taaccgcatt tctaacaggc ggttaaagta tcaaagtttg acccttccct
     1441 taaaaatgca gtggtcaatt gaccgaattt tatgcagaag tgggtttttg agttttgggg
     1501 tttgaaacga gaaaaaagag gtcgatttcg acctcttttt ttgatgtttc ttcttatctt
     1561 gatactatag gcaactattt ctgcgaagaa atcggggcta tagtatgggt ctatcccttg
     1621 tggctctaag gaagaacaaa aaaaaagatt gctttttctt ccctagtatt ttatagtttt
     1681 aattgactag aaaaaaacta aactagaaag gagagcaatc tattttttgt tatcggcttt
     1741 tcagcctttt ttgtatacaa aatttgtaga ttcagtatag caagatgaaa aagaaaaagc
     1801 aagatttgat taacggaaca tttcgagaaa aaaagaaaaa tttgaaaaaa gtggtggcat
     1861 ttagtgataa tcgaatttct cccaaaatgc gtgaattgat gacaggctgt ggttcatatt
     1921 tagaatttat tgcaacgatt gataaggaga aaaagaaatt ggtccaagct cacttttgta
     1981 aaaatcgttt ctgtccgtta tgtgcttggc gtaaagctcg taaggattcg atgatgttgt
     2041 cgattatgat gcaagctatt gcggaagaaa agcagtatca atttattttt atgacgttga
     2101 cgacaccgaa tgtaaaagcg gaatgtttga acgatgaaat tgatttgttt aatcatgcat
     2161 tgaaaaagat gtttatgcgc aaacgggtta agacttcgat taaaggctat gtgcgaaaat
     2221 tggaaatcac gtacaacaaa aaacggaatg actataaccc gcattttcac ttgattttgg
     2281 cagtaaataa atcttatttc acggataaag attattatat caagcaatcg gaatggttag
     2341 atttgtggcg ggaagtgacc ggaaaaacgg gaattaatcc ggatggtacc gacgaaatta
     2401 cccagttgga tattcgcaag gtcaaagggt tccaacaaga aaaagcagta caggaagttg
     2461 cgaaatattc ggcaaaagat tttgaactga ccgaaagtca ggaagtgttt gacacattct
     2521 atcatgcaat gaaaggtcgt cagttgatta cgtttaacgg tgtattcaaa gaatacaaga
     2581 aaaaatatga gtcgggtgac cttgatcgtt ataagaaaaa agatgagaat gaatattttt
     2641 ggtttttgac tgcttcgtgg atgaggaaag aatcgaaata tgcggttgat tatcgtgaga
     2701 tgagtgctga tgaaagaaat tatttttcag gaatgtatgt cgatgaaaaa tctgttgagg
     2761 gggaaaatga atgactgatt caacggataa aatgacaatt aaggcgcttg ctgatgaact
     2821 aggaataacc aaaaatacag tgagaaatta tctagtcaaa gccggatatg atcttgctcg
     2881 gtacaagaaa aatggaatta tcttgctaga caaagagttg attggtgttg ctcggtcaat
     2941 ttatcggtca aaaggtggtc aattgactgg tcatttaccg gtcaatagca cgggcagtga
     3001 ttttcctttg gaaaaagaga atgagttttt gcgtgatcaa ttagctgaga aggacaaaca
     3061 tatttctgaa ttaacagaaa tgattcgtga tcaacaaaaa ttgaccctgc ttcagcaaca
     3121 aaaaaacgat cagttgttac tagaaaatca agaattaaaa aatcgaaaat ggtggcaatt
     3181 ctggaagtga gatgtgacat ggataaaatt gatttgagag aagaaacagt caatagaatt
     3241 gaagtgatgt atgaacggtt agctgattat ttgaatcttt cggatgaaga taattatagt
     3301 gagatgcttg aacgaatgat ggatgttctc aactcggtta tcaatgctga tctagcaaaa
     3361 tcttcagttt tgactaatga atttgttcat aagcatttag cgcaaacaac tgatgaagct
     3421 gaaaaagaat tttggttgaa attaatgagt catattatgc agttaaacca aatttccgtt
     3481 attaattcca aagaaaaggg gatgtagttt atgggaatga ctttagcaga tattaaagtg
     3541 caagaagaaa aattaaaaaa agaacaggcg aaacttcgcc aacagaagaa acgattgatt
     3601 gagaaagaaa atgctgcaat gggcaaggct cttcgcaagc gttttgggtt tgaatctttt
     3661 gctgattttg agcggtggtt atcgtcaatt tctgacgatc agcaacacga aaaatcagtg
     3721 gataatgagt ggcttgctga tgaaaaatca gcgccaagcg aacgagatta tcccaatgaa
     3781 tatgacggct tactcggagt gatgccgagt aaaaaaagtc agatgaatga gagtaaattt
     3841 atgtcaattt ttaatgacgt gaatttacga taagctatta ttttgcgtga agcaaaataa
     3901 agcgtaaaag gagttgagag cgtgacacgc tttcggctcc ttttttcgtt gtcacttgtg
     3961 acagcgaaat ccctcggaga gcgtttggaa ttgtgacagt catgtcacaa ttaggaaaac
     4021 gttactcttt gacaaagagt aacagaaagg tttacactct ttttattagc gacagcgcga
     4081 aggaggggtc taacttgggg tttagtattt cgttcaaaaa gggaacaaag aatacaagca
     4141 tttctcataa taatcgtgag ttaactgata gccaaaaaat caatgactgg cataagcata
     4201 ttgatttcac aaaatcggat gaaaatatct atttggaaca aacaaatatt cgtgaaaaat
     4261 atgaagaatt attcggtgaa gccgtagaaa aatataatgc aaagcagaaa agagcc
//
