LOCUS       CP035664                4316 bp    DNA     circular BCT 20-APR-2023
DEFINITION  Enterococcus faecium strain UAMSEF_20 plasmid unnamed4, complete
            sequence.
ACCESSION   CP035664
VERSION     CP035664.1
DBLINK      BioProject: PRJNA518133
            BioSample: SAMN10863493
KEYWORDS    .
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, e0490122 (2023) In press
   PUBMED   36995227
  REMARK    Publication Status: Available-Online prior to print
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                   :: 580.0x
            Sequencing Technology :: Oxford Nanopore MiniION; Illumina NextSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 02/05/2019 10:04:23
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 4.7
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 3,478
            CDSs (total)                      :: 3,385
            Genes (coding)                    :: 3,057
            CDSs (with protein)               :: 3,057
            Genes (RNA)                       :: 93
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 71
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 328
            CDSs (without protein)            :: 328
            Pseudo Genes (ambiguous residues) :: 0 of 328
            Pseudo Genes (frameshifted)       :: 188 of 328
            Pseudo Genes (incomplete)         :: 104 of 328
            Pseudo Genes (internal stop)      :: 74 of 328
            Pseudo Genes (multiple problems)  :: 34 of 328
            ##Genome-Annotation-Data-END##
            Bacteria and source DNA available from Tip's lab.
            Annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (released 2013). Information about the Pipeline can be
            found here: https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
FEATURES             Location/Qualifiers
     source          1..4316
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="UAMSEF_20"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="unnamed4"
                     /geo_loc_name="USA:Arkansas"
                     /collection_date="2018-09-26"
     gene            join(4108..4316,1..211)
                     /locus_tag="EWH22_00540"
     CDS             join(4108..4316,1..211)
                     /locus_tag="EWH22_00540"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173821.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QCV42335.1"
                     /translation="MTDSTDKMTIKALADELGITKNTVRNYLVKAGYDLARYKKNGIIL
                     LDKELIGVARSIYRSKGGQLTGHLPVNSTGSDFPLEKENEFLRDQLAEKDKHISELTEM
                     IRDQQKLTLLQQQKNDQLLLENQELKNRKWWQFWK"
                     /name="hypothetical protein"
     gene            220..528
                     /locus_tag="EWH22_00545"
     CDS             220..528
                     /locus_tag="EWH22_00545"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173820.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QCV42339.1"
                     /translation="MDKIDLREETVNRIEVMYERLADYLNLSDEDNYSEMLERMMDVLN
                     SVINADLAKSSVLTNEFVHKHLAQTTDEAEKEFWLKLMSHIMQLNQISVINSKEKGM"
                     /name="hypothetical protein"
     gene            532..894
                     /locus_tag="EWH22_00550"
     CDS             532..894
                     /locus_tag="EWH22_00550"
                     /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="QCV42336.1"
                     /translation="MGMTLADIKVQEEKLKKEQAKLRQQKKRLIEKENAAMGKALRKRF
                     GFESFADFERWLSSISDDQQHEKSVDNEWLADEKSAPSERDYPNEYDGLLGVMPSKKSQ
                     MNESKFMSIFNDVNLR"
                     /name="hypothetical protein"
     gene            1116..2522
                     /locus_tag="EWH22_00555"
     CDS             1116..2522
                     /locus_tag="EWH22_00555"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016173818.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="recombinase"
                     /protein_id="QCV42337.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDSQKINDWHKHIDFTKSDENI
                     YLEQTNIREKYEELFGEAVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGTL
                     DDFRTTRDDGSSTGISEQQAEQNRVIANKILVEYFKEFKERNPSLSVYNAVIHNDEVSP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALQQQGLRADKENGRVIWNNFRNQEVESIERLMA
                     DFGWERELVGTNKIKDVHEYKEIMSEISELRQTAVKERESVSDELGYISRQREENEREK
                     ALVASERAKIEEEKKNMLNVKKEMAVIFQKDIVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVATLEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKKAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQHK
                     LERSEDEIEW"
                     /name="recombinase"
     gene            3122..4111
                     /locus_tag="EWH22_00560"
     CDS             3122..4111
                     /locus_tag="EWH22_00560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002349057.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication protein"
                     /protein_id="QCV42338.1"
                     /translation="MKKKKQDLINGTFREKKKNLKKVVAFSDNRISPKMRELMTGCGSY
                     LEFIATIDKEKKKLVQAHFCKNRFCPLCAWRKARKDSMMLSIMMQAIAEEKQYQFIFMT
                     LTTPNVKAECLNDEIDLFNHALKKMFMRKRVKTSIKGYVRKLEITYNKKRNDYNPHFHL
                     ILAVNKSYFTDKDYYIKQSEWLDLWREVTGKTGINPDGTDEITQLDIRKVKGFQQEKAV
                     QEVAKYSAKDFELTESQEVFDTFYHAMKGRQLITFNGVFKEYKKKYESGDLDRYKKKDE
                     NEYFWFLTASWMRKESKYAVDYREMSADERNYFSGMYVDEKSVEGENE"
                     /name="replication protein"
     Typing          1117..2519
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.863"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ggtcaatagc acgggcagtg attttccttt ggaaaaagag aatgagtttt tgcgtgatca
       61 attagctgag aaggacaaac atatttctga attaacagaa atgattcgtg atcaacaaaa
      121 attgaccctg cttcagcaac aaaaaaacga tcagttgtta ctagaaaatc aagaattaaa
      181 aaatcgaaaa tggtggcaat tctggaagtg agatgtgaca tggataaaat tgatttgaga
      241 gaagaaacag tcaatagaat tgaagtgatg tatgaacggt tagctgatta tttgaatctt
      301 tcggatgaag ataattatag tgagatgctt gaacgaatga tggatgttct caactcggtt
      361 atcaatgctg atctagcaaa atcttcagtt ttgactaatg aatttgttca taagcattta
      421 gcgcaaacaa ctgatgaagc tgaaaaagaa ttttggttga aattaatgag tcatattatg
      481 cagttaaacc aaatttccgt tattaattcc aaagaaaagg ggatgtagtt tatgggaatg
      541 actttagcag atattaaagt gcaagaagaa aaattaaaaa aagaacaggc gaaacttcgc
      601 caacagaaga aacgattgat tgagaaagaa aatgctgcaa tgggcaaggc tcttcgcaag
      661 cgttttgggt ttgaatcttt tgctgatttt gagcggtggt tatcgtcaat ttctgacgat
      721 cagcaacacg aaaaatcagt ggataatgag tggcttgctg atgaaaaatc agcgccaagc
      781 gaacgagatt atcccaatga atatgacggc ttactcggag tgatgccgag taaaaaaagt
      841 cagatgaatg agagtaaatt tatgtcaatt tttaatgacg tgaatttacg ataagctatt
      901 attttgcgtg aagcaaaata aagcgtaaaa ggagttgaga gcgtgacacg ctttcggctc
      961 cttttttcgt tgtcacttgt gacagcgaaa tccctcggag agcgtttgga attgtgacag
     1021 tcatgtcaca attaggaaaa cgttactctt tgacaaagag taacagaaag gtttacactc
     1081 tttttattag cgacagcgcg aaggaggggt ctaacttggg gtttagtatt tcgttcaaaa
     1141 agggaacaaa gaatacaagc atttctcata ataatcgtga gttaactgat agccaaaaaa
     1201 tcaatgactg gcataagcat attgatttca caaaatcgga tgaaaatatc tatttggaac
     1261 aaacaaatat tcgtgaaaaa tatgaagaat tattcggtga agccgtagaa aaatataatg
     1321 caaagcagaa aagagccgat agaaaaatcg aggactattt agcaaaggtt cgcaaggata
     1381 aaaaattgga accacagcga gaatttatcg tgcaaattgg tactcttgat gattttcgta
     1441 ctactcgtga tgatggttct tctactggca tatcggaaca acaagcagaa caaaatcgag
     1501 tgattgccaa caaaatttta gttgagtatt tcaaagaatt taaagaacgg aatcctagtt
     1561 tatccgtcta caatgctgtt attcataatg acgaagtaag tccgcacctg catttgaata
     1621 ttgttcctgt tgctgaaggg tataaacggg gtgttcaaaa gcaaccaagt tttaacaaag
     1681 ccttgcaaca gcagggttta cgagcagata aagagaatgg tcgagtgatt tggaataatt
     1741 ttaggaatca ggaagttgag tcaattgaac gtttgatggc agattttggt tgggagcgtg
     1801 agttagtcgg tactaacaaa atcaaagatg ttcacgaata taaagaaatc atgagcgaga
     1861 tttcagaatt gcgtcaaacg gccgtaaaag agcgtgagag cgtttctgat gagttggggt
     1921 atatttctag gcaaagagaa gaaaacgagc gagaaaaggc tctggtggct tctgagagag
     1981 caaagattga agaagagaag aaaaatatgc tgaatgtaaa aaaagagatg gcggtcattt
     2041 tccaaaaaga tattgttcct ttagaaagtt tcaagaggct tcctgatggt tcgtatcatt
     2101 tatctgggaa tgattttgtt gatttgtatc aacgagctac gagagcaaca aatgccaaga
     2161 gaaatgctga taacatgagt gagcaatatt tacagatgct tgagcaaaat acagaattaa
     2221 atgagtatgt agctacattg gaagaagagc gtcatttgtc tggtagaaaa caattagcag
     2281 atttacaagt ggaaaataaa aagctgaaag aagaaaatcg ctctttacgc cagcgtttag
     2341 agcgattaaa aaaagcattt caaaaatcga tcactcgttt gtctatccgt tttggtcttg
     2401 cagaaaagga tatggggctt tctgaggaat tagaagtatt agagcaggag aaaaccttat
     2461 tttatcgtca aaacgtctca cagcataaat tagagcgttc tgaagatgag atcgagtggt
     2521 agttacgatg tgcagtcaac ggtaccggag gcggtctgtg ccgaggataa ggagttgacg
     2581 gctaaaccac tagcctatta agctgacatt tgctaaaaaa tggcaagtcc attttttggc
     2641 caacctagcg ttagcgaaag tttgggggcg cccttttcaa agggagcggt tttatttttg
     2701 catgactaag aatgagtggg aaaaacttaa ccgcatttct aacaggcggt taaagtatca
     2761 aagtttgacc cttcccttaa aaatgcagtg gtcaattgac cgaattttat gcagaagtgg
     2821 gtttttgagt tttggggttt gaaacgagaa aaaagaggtc gatttcgacc tctttttttg
     2881 atgtttcttc ttatcttgat actataggca actatttctg cgaagaaatc ggggctatag
     2941 tatgggtcta tcccttgtgg ctctaaggaa gaacaaaaaa aaagattgct ttttcttccc
     3001 tagtatttta tagttttaat tgactagaaa aaaactaaac tagaaaggag agcaatctat
     3061 tttttgttat cggcttttca gccttttttg tatacaaaat ttgtagattc agtatagcaa
     3121 gatgaaaaag aaaaagcaag atttgattaa cggaacattt cgagaaaaaa agaaaaattt
     3181 gaaaaaagtg gtggcattta gtgataatcg aatttctccc aaaatgcgtg aattgatgac
     3241 aggctgtggt tcatatttag aatttattgc aacgattgat aaggagaaaa agaaattggt
     3301 ccaagctcac ttttgtaaaa atcgtttctg tccgttatgt gcttggcgta aagctcgtaa
     3361 ggattcgatg atgttgtcga ttatgatgca agctattgcg gaagaaaagc agtatcaatt
     3421 tatttttatg acgttgacga caccgaatgt aaaagcggaa tgtttgaacg atgaaattga
     3481 tttgtttaat catgcattga aaaagatgtt tatgcgcaaa cgggttaaga cttcgattaa
     3541 aggctatgtg cgaaaattgg aaatcacgta caacaaaaaa cggaatgact ataacccgca
     3601 ttttcacttg attttggcag taaataaatc ttatttcacg gataaagatt attatatcaa
     3661 gcaatcggaa tggttagatt tgtggcggga agtgaccgga aaaacgggaa ttaatccgga
     3721 tggtaccgac gaaattaccc agttggatat tcgcaaggtc aaagggttcc aacaagaaaa
     3781 agcagtacag gaagttgcga aatattcggc aaaagatttt gaactgaccg aaagtcagga
     3841 agtgtttgac acattctatc atgcaatgaa aggtcgtcag ttgattacgt ttaacggtgt
     3901 attcaaagaa tacaagaaaa aatatgagtc gggtgacctt gatcgttata agaaaaaaga
     3961 tgagaatgaa tatttttggt ttttgactgc ttcgtggatg aggaaagaat cgaaatatgc
     4021 ggttgattat cgtgagatga gtgctgatga aagaaattat ttttcaggaa tgtatgtcga
     4081 tgaaaaatct gttgaggggg aaaatgaatg actgattcaa cggataaaat gacaattaag
     4141 gcgcttgctg atgaactagg aataaccaaa aatacagtga gaaattatct agtcaaagcc
     4201 ggatatgatc ttgctcggta caagaaaaat ggaattatct tgctagacaa agagttgatt
     4261 ggtgttgctc ggtcaattta tcggtcaaaa ggtggtcaat tgactggtca tttacc
//
