LOCUS       CP035663                6303 bp    DNA     circular BCT 20-APR-2023
DEFINITION  Enterococcus faecium strain UAMSEF_20 plasmid unnamed3, complete
            sequence.
ACCESSION   CP035663
VERSION     CP035663.1
DBLINK      BioProject: PRJNA518133
            BioSample: SAMN10863493
KEYWORDS    .
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 6303)
  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 6303)
  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..6303
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="UAMSEF_20"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="unnamed3"
                     /geo_loc_name="USA:Arkansas"
                     /collection_date="2018-09-26"
     gene            627..713
                     /locus_tag="EWH22_00495"
     CDS             627..713
                     /locus_tag="EWH22_00495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011302749.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type I toxin-antitoxin system Fst family toxin"
                     /protein_id="QCV42334.1"
                     /translation="MFERFICPLLVEVCVSLFSYWLNNRNKK"
                     /name="type I toxin-antitoxin system Fst family toxin"
     gene            complement(834..1523)
                     /locus_tag="EWH22_00500"
     CDS             complement(834..1523)
                     /locus_tag="EWH22_00500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002298772.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QCV42326.1"
                     /translation="MAFYLPYLLISASILGIIWLSYKAYQTRYSLKGSKIRFKRFLLVG
                     VIFALSIVLSGLFGVLEGNKRVSRSILLGDITQKYEAACDKKKKEQALAQKMEEFTACY
                     EDMNNIFVDQEKRLTDKNMKKLTRFYQNLPEKQQKEVQEKYEQVKKDVQYFKDTQTEEA
                     CCNLFSDTIPFSTSEQERKERQQSVTYERYETLLQQATNIQNPTKKETALNYLESVKEW
                     LDQQQQN"
                     /name="hypothetical protein"
     gene            complement(1530..1808)
                     /locus_tag="EWH22_00505"
     CDS             complement(1530..1808)
                     /locus_tag="EWH22_00505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002354385.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QCV42327.1"
                     /translation="MNEEQTTNKNYRSKTLKDIENEIKRQRAFLAPYTQERIQTTMDSQ
                     VKKLHQALLDQRNQEQKKALIQRSMDILAPLCCLVLTLLAFWLVWGE"
                     /name="hypothetical protein"
     gene            complement(1768..2682)
                     /locus_tag="EWH22_00510"
     CDS             complement(1768..2682)
                     /locus_tag="EWH22_00510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002340563.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase"
                     /protein_id="QCV42328.1"
                     /translation="MATVKVSRTTSCSRAINYAEPRATVKTGINCDIDYAKSEMKQIRT
                     LYGKDDRVQAHLLIQSFRPGEITAEKANQLGAEYAKKIAPNHQIAIYTHTDKDHIHNHI
                     VINSVNLETGKKFQAHGQAFLNKCYDLNDEICLEHDLTITERGKKTEKRTMSEIKLKEK
                     NEPVWKDEIRFAIDQTMKNKKTRTYTQFCDSLKTFGIHCLNRGKNFTYELVHKKKKVRS
                     NKLGKDYEKETILHELDRRERTYNQQRTNELRRARASIRETAEEVRREQRTFTPEQSEI
                     RPTRRNHEQHVERGTDHQQELSL"
                     /name="relaxase"
     gene            complement(2664..3044)
                     /locus_tag="EWH22_00515"
     CDS             complement(2664..3044)
                     /locus_tag="EWH22_00515"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002348702.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="QCV42329.1"
                     /translation="MSEQHQNLASDHSKKYTYRSEPKQISFRVSESEFAKLKQSAEALQ
                     MSVPAFVKAKAQNARLVTPKVAPDIAQAIARDLAKAGGNINQIAKWCNTHQHDVAPDDA
                     QRLSENLKIMQKELQKIWQQLK"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            complement(3366..3569)
                     /locus_tag="EWH22_00520"
     CDS             complement(3366..3569)
                     /locus_tag="EWH22_00520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002307460.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QCV42330.1"
                     /translation="MFLISKSLKSLKTFTKKNPQIATIRIFIFAIAVAIIVNMLSGGQL
                     YKSGLFLVLILVVLDIIKSKKK"
                     /name="hypothetical protein"
     gene            complement(3581..4114)
                     /locus_tag="EWH22_00525"
     CDS             complement(3581..4114)
                     /locus_tag="EWH22_00525"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002334266.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QCV42331.1"
                     /translation="MKKFTLGVALLTIGAVVLPSTTIVYASENSQVVSLNENNATENVV
                     IEYTEDGMVVTKYEDGYSAEDFANSSDIMTRAAVARWGKKEYTNIAVTTGVAANAINAA
                     FWAGGKASTSMFGIPGWAIGALLTGASWTKKGASPGNAVAKEWDKNGNGWIGFYYQRGY
                     DAAGRVVATRYSTL"
                     /name="hypothetical protein"
     gene            complement(4750..5283)
                     /locus_tag="EWH22_00530"
     CDS             complement(4750..5283)
                     /locus_tag="EWH22_00530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002292473.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF536 domain-containing protein"
                     /protein_id="QCV42332.1"
                     /translation="MQPQETFTIKELSELFKMSRQAISKHIQKLDSSMIAKNERGYKVV
                     LRSGVLQLARNLGNQMLLDRLHEYEQDNDKNVNIPSKNVVTNKLLDQLREENEFLREQL
                     ALREQNNSHIQKLLDQQQQLTLQANKQIEKLQEKLQLTYTEEAPENDSTTLSEATETID
                     KQIDTEKKWWQLWK"
                     /name="DUF536 domain-containing protein"
     gene            complement(5304..6254)
                     /locus_tag="EWH22_00535"
     CDS             complement(5304..6254)
                     /locus_tag="EWH22_00535"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002303559.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="RepB family plasmid replication initiator
                     protein"
                     /protein_id="QCV42333.1"
                     /translation="MANEIVKYHHELNTIPLRKFTPVEMNLFFSIVSRMREKGDKTVRL
                     TFDQLKDLSNYKATANNRFINDLEMTYDKLMDLRFGKRSANGLDIDRFVMFSEFKIRGT
                     AKDPYVDIQVYEKALPLLNNLDEWVRYSLQQFNELQSSYAKTMFRLLKQYRTKGFAYFS
                     KEDFHELLDIPKSYWNNQANVDNRVIKPIRQELTAIFKGLSIKKKYGKGRGKPVVGYQF
                     TFKPEIKKADDFNKHAPTKEEQNKALALADKQKEYEEPATTINEKIKQKKRELELLQQI
                     KQLEKEKEALEKQTESALSKKEKKSLLSDLDNLFQ"
                     /name="RepB family plasmid replication initiator protein"
     Typing          complement(5305..6253)
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.953"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(1772..2682)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.079"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tttgtctgtg ataatgcata ttataacata cgtgagtgca aaaaaagagt ttaaaagcag
       61 acaaaatgta gtttaaaagc agacaaaatg tagtttaaaa gcagacaaaa tgtagtttaa
      121 aagcagacaa aatgtagttt ataaaacgct gtatccattg aaggagtaag gacacagccg
      181 acggtaaaga ggtttaaaaa aaggtttaaa aagagattat aaaagagggt gacaaaattt
      241 cccgcctaaa aaccacttct tttttctacc aacaggttcg cgcatttttc aaaactgcca
      301 attcaaaacc ttgctcccta cggtcgctaa aaaagtgtga tcgctatgct ctcacattgt
      361 actgcgcagt cgcctaaagg ctcctttgct aaaaacaagt cagtaacgga ggtgggggaa
      421 gcctctgata gctcgtctaa gtcgttttaa gacagtcttg ggtaaaaaac cttatcttgt
      481 tcttaaagcg ccttacaggc ggtcagggca agccctaaca acccgaaaat aagggatact
      541 taaaaacacc acacagattt tattttgtaa ggtataataa cttgtcgcct atccgacagt
      601 cttgcgactg gaaggaggtg tatctaatgt ttgaacggtt catttgcccc cttcttgtag
      661 aagtttgtgt ctctttattc agttattggt tgaataaccg aaacaagaag taaaatcaat
      721 aaaggcgaca tcaacctgaa aaaaagcccc agagaatccg acctctctgg ggctttcgtg
      781 tatctaatgt ttgatcattt gcaggttcag tttaacatga ttgctaatca aattcaattt
      841 tgttgttgct gatccaacca ttccttgaca ctttctagat aatttaatgc cgtttctttt
      901 ttcgttggat tttgtatgtt tgttgcttgc tgaagcagtg tttcataacg ttcgtatgtg
      961 accgattgtt gccgttcttt tcgttcttgt tcactggttg aaaaagggat tgtatcgcta
     1021 aataagttac aacaagcttc ttctgtctgc gtatctttaa aatattgcac gtcttttttt
     1081 acttgctcat atttttcttg tacctctttt tgctgttttt ctggtaagtt ttgataaaaa
     1141 cgagtgagtt ttttcatgtt tttatctgtt aaacgtttct cttgatccac aaaaatattg
     1201 ttcatgtcct cataacaagc ggtaaattcc tccatttttt gtgctaatgc ttgctctttt
     1261 ttctttttat cacatgctgc ttcatacttt tgagtgatat cccctaataa aatgcttctt
     1321 gaaacacgtt tattaccctc taaaacgccg aataaaccac ttaaaacgat tgataaggca
     1381 aatataaccc cgaccaataa aaatcgctta aatcgaattt tagagccttt taatgaatat
     1441 cttgtttgat aagccttata gctaagccaa ataattccta aaatactggc agaaatgagt
     1501 agatagggta aatagaatgc catgtctgtt tattctcccc ataccaacca aaaggctaat
     1561 aatgttagta ctaagcaaca taagggggca agaatatcca tcgatcgttg aattaaagcc
     1621 tttttttgtt cttggtttcg ctggtctaat agcgcttggt ggagtttttt gacttgtgaa
     1681 tccatcgtag tttgtatcct ttcttgggta taaggcgcaa gaaaggcacg ttgtctcttt
     1741 atttcgtttt cgatgtcttt taacgtttta gagcgataat tcttgttggt ggtctgttcc
     1801 tcgttcaacg tgttgttcat ggtttcttcg agtcggtcta atttccgatt gttcaggcgt
     1861 aaaagttcgt tgttctcttc gtacttcttc tgcagtttcg cgaatgctag ctcgagctct
     1921 tcgtagctcg ttggttcgtt gttgattgta ggttcgttct cgtctgtcca gctcatgtaa
     1981 aatcgtctcc ttttcgtaat cctttcctag tttgttggat cgtacttttt tctttttgtg
     2041 gaccaattcg taagtaaaat tttttccgcg attcaagcaa tgaatgccga atgttttaag
     2101 tgaatcacaa aattgggtat acgttcgagt ttttttgttt ttcattgttt gatcaatcgc
     2161 aaaccgaatt tcgtctttcc aaaccggttc atttttttct tttaatttaa tttcagacat
     2221 ggttcgtttt tcggttttct ttcctcgttc cgtgattgtt aagtcatgtt caagacaaat
     2281 ctcgtcattt aggtcataac atttgtttaa aaatgcttgc ccatgggctt gaaatttttt
     2341 cccagtttca agattaacgg agttaatgac aatgtgatta tgaatatggt ctttgtctgt
     2401 atgtgtgtaa atcgcgattt ggtggttagg ggctattttt ttcgcatact ctgcccctag
     2461 ttgattggct ttttcagcgg taatttctcc tggtcgaaag gactgaatca ataagtgtgc
     2521 ttgtacacga tcgtcttttc cataaagcgt gcgtatttgt ttcatttcac ttttggcata
     2581 atcaatgtca cagtttattc ctgttttgac ggttgctcgt ggttctgcgt aattgattgc
     2641 tcggctacat gaagtggttc gacttacttt aactgttgcc atatcttttg tagctccttt
     2701 tgcatgattt ttaggttttc ggataaacgt tgagcatcat caggagcaac gtcgtgttgg
     2761 tgtgtattgc accacttggc aatttgattg atattccctc cagctttggc taaatcgcgc
     2821 gcgattgcct gggcaatgtc tggcgccact ttcggtgtca ccagacgcgc gttttgtgcc
     2881 ttggctttca cgaaagccgg cacactcatt tgcaaagctt cagctgactg cttcagcttt
     2941 gcaaattcgg attcgctcac tcgaaaactg atttgttttg gctcggatcg ataggtatat
     3001 tttttagaat gatcgctagc caaattttga tgttgttcgc tcataagtcc caccctttca
     3061 gtacgtccta cggacgtatc gttcgcaata ccattgtacc taaaaaggta caatgagtaa
     3121 agctcactaa aagggtttgg caagctctat atttgctagc caaatacctc cgtatttggt
     3181 gcaaataacc gcttgtcaaa ggagcgcaag ctcccccttg aatccccctc aaaatccacg
     3241 ctccacaata caaaaaaagg ctagcatttg ctagccactt tttgtaaagt ttcgcttatt
     3301 tcaccgaagg tgaaattgtt gctttgtaat attcaaacaa ccctattctt ctaaaatgta
     3361 tcgatttatt tttttttaga ctttattatg tctaagacaa ctaagattaa cactaaaaat
     3421 aaaccagatt tgtataattg ccctccgctt agcatattaa caattatagc aacagctata
     3481 gcaaatataa aaatacgaat agtagctatt tgcggattct ttttagtaaa tgtttttaat
     3541 gattttaatg atttagatat caaaaacatc actccttaac ttataacgtt gaatatctag
     3601 tagctacaac tcttccagct gcatcatatc ccctttggta ataaaatcca atccagccat
     3661 taccattttt gtcccattct tttgcaactg cattccctgg agaagcacct tttttagtcc
     3721 aacttgcacc tgttaacaaa gcaccaattg cccaacctgg gataccaaac atagaagtgc
     3781 tagctttccc tcctgcccaa aaggcagcat taatagcatt agcagctact ccagtggtta
     3841 cagcaatatt tgtatattcc tttttgcccc atcttgcaac tgcagctctt gtcatgatat
     3901 ctgaagaatt tgcaaaatct tccgcactat aaccatcctc atatttagtt acgaccatac
     3961 catcttcagt gtactcaata actacatttt cagtagcatt gttttcgttt aatgatacca
     4021 cttgggaatt ttctgaagca taaactatag tagttgacgg taaaacaact gccccaatag
     4081 ttaacaaagc tacccctaaa gtaaattttt tcatagaatt tcctcctgat acagaaaaat
     4141 atatagaaaa cgttttcttt gtgaaaatca taaaacaaaa ggtataggct tgtcaatatt
     4201 ttatttagta aagataattt atatttttga taatgtggta tagttagaat gcattaggaa
     4261 aatatgttat attaaattct tgttgacata atgtacacta tgccaagtag cccttgtatc
     4321 aaccgataca gaggctcact ttgtgatttt cgattggtct aggtcaaaag ctctttttaa
     4381 gcttgatttt ctgcggttgc ttctttccgt ttctttgtga atttttacca gtcatttttt
     4441 actgggttgt tatttttaat aaaatatgat aaatttttgg tagcgcttca taagcgcgtt
     4501 gctttttcaa gaataaacac tcattatttt ttaactggct gctcgaaaga gcagtctttt
     4561 ttattattta tctgtttctt ttacaaacaa ttcttcgtta ggactgttgt aataatttgg
     4621 attcaatttc aattcaccat gtttattccc tttattgatc actgacaata acatcggact
     4681 gaatcctaga attcctagta aaatagaacc gaatagaaga ttttttcttg tcatgaatgt
     4741 tccctccagt tatttccaaa gttgccacca ttttttttca gtatcaattt gtttgtctat
     4801 tgtttctgtt gcttcagaaa gagtcgttga gtcattctct ggagcttctt ctgtataagt
     4861 caactgtagt ttttcttgca gtttttcgat ttgtttgttg gcttgtaggg tgagttgttg
     4921 ttgctggtcg agtagttttt gtatatgaga attattttgc tctctgaggg caagttgttc
     4981 tcgtaaaaat tcattttctt cacgcaactg atctagcaac ttgtttgtaa ccacgttttt
     5041 gcttggtata ttaacatttt tatcgttgtc ttgttcgtac tcgtgcaacc tatctagcaa
     5101 catttggttg cctaagttgc gagcaagttg caatactcca gaacgcaata caaccttata
     5161 accacgctca tttttagcta tcatggaaga atctaatttt tggatatgtt tcgatattgc
     5221 ttgcctactc atcttaaaaa gttctgacaa ttcctttatt gtaaaggttt cttgtggttg
     5281 catactggtt gcctcctagg ttgctactgg aataaattat ctaaatcaga taataaactt
     5341 tttttctctt ttttcgaaag tgcggactct gtttgttttt caagagcttc tttctctttt
     5401 tctagttgtt tgatttgttg gaggagttca agttctcgtt tcttctgttt gattttttcg
     5461 ttaattgttg tagcaggttc ttcgtattct ttttgtttat cagctaaagc caatgcttta
     5521 ttttgttctt ctttggttgg tgcatgttta ttaaaatcat ctgctttttt gatttctggt
     5581 ttaaacgtaa attgatagcc aacgacaggt tttcctcgcc cttttccgta tttctttttg
     5641 attgataatc ctttgaagat tgcggttaat tcctgtcgta taggctttat aacacgatta
     5701 tcaacgtttg cttggttgtt ccagtaactt tttggaatat ctaatagttc atgaaaatcc
     5761 tctttagaaa aataagcaaa acctttagtt cgatattgtt ttagtaatcg aaacatagtc
     5821 tttgcatagc tactttgtaa ttcgttaaat tgttggagtg aatagcgaac ccactcatct
     5881 aaattgttta gtaaaggtaa agctttttcg taaacttgta tgtctacata tggatcttta
     5941 gcagttccac gtattttaaa ctcactaaac ataacgaatc tatctatatc gagcccatta
     6001 gcacttcttt taccaaaacg taaatccatt aatttatcat aagtcatttc taaatcatta
     6061 atgaaacgat tattagcagt tgctttataa ttacttaaat cttttagttg gtcaaaagta
     6121 agacggactg ttttatcgcc tttttcgcgc attctagaca caatagagaa aaatagattc
     6181 atttcaactg gtgtaaattt ccgcaacgga atggtattta attcatgatg gtatttcacg
     6241 atttcatttg ccaaagatat tcctccttac tccttcaatg gatacagacg ttataaacaa
     6301 cgt
//
