LOCUS       NZ_CP059781             3866 bp    DNA     circular CON 06-NOV-2023
DEFINITION  Enterococcus faecium strain A3895 plasmid pA3895_P9, complete
            sequence.
ACCESSION   NZ_CP059781
VERSION     NZ_CP059781.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14675384
            Assembly: GCF_012933265.2
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 3866)
  AUTHORS   Veeraraghavan,B., Vasudevan,K., Arumugam,A., Solaimalai,D. and
            Bakthavatchalam,Y.D.
  TITLE     Complete genome of vancomycin resistant Enterococcus faecium
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3866)
  AUTHORS   Veeraraghavan,B., Vasudevan,K., Arumugam,A., Solaimalai,D. and
            Bakthavatchalam,Y.D.
  TITLE     Direct Submission
  JOURNAL   Submitted (09-JUL-2020) Clinical Microbiology, Christian Medical
            College, Ida Scudder Road, Vellore, Tamil Nadu 632004, India
REFERENCE   3  (bases 1 to 3866)
  AUTHORS   Veeraraghavan,B., Solaimalai,D., Vasudevan,K. and Arumugam,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-APR-2020) Department of Clinical Microbiology,
            Christian Medical College and Hospital, Ida Scudder Road, Vellore,
            Tamil Nadu 632004, India
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2020
            Assembly Method :: CANU v. v. 1.7; UNICYCLER HYBRID v. v. 0.4.6
            Assembly Name                     :: A3895
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 40.42x
            Sequencing Technology :: Illumina HiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/06/2023 04:47:14
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 3,060
            CDSs (total)                      :: 2,970
            Genes (coding)                    :: 2,868
            CDSs (with protein)               :: 2,868
            Genes (RNA)                       :: 90
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 68
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 102
            CDSs (without protein)            :: 102
            Pseudo Genes (ambiguous residues) :: 0 of 102
            Pseudo Genes (frameshifted)       :: 35 of 102
            Pseudo Genes (incomplete)         :: 68 of 102
            Pseudo Genes (internal stop)      :: 25 of 102
            Pseudo Genes (multiple problems)  :: 20 of 102
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP059781.1.
            Bacteria and source DNA available from Christian Medical College.
            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..3866
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="A3895"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pA3895_P9"
                     /geo_loc_name="India: Vellore"
                     /lat_lon="12.9165 N 79.1325 E"
                     /collection_date="2019"
                     /collected_by="CMC Vellore"
     gene            complement(join(3561..3866,1..1101))
                     /locus_tag="HI845_RS15140"
                     /old_locus_tag="H4J14_015135"
     CDS             complement(join(3561..3866,1..1101))
                     /locus_tag="HI845_RS15140"
                     /old_locus_tag="H4J14_015135"
                     /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_127837500.1"
                     /translation="MGFSISFKKGTKNTSISHNNRELTDRQKTNDWHKHIDFTKSDENI
                     YLEQTNLADKYEELFGEVVEKYNAKQKRADRKIEDYLAKVRKDKKLEPQREFIVQIGIL
                     DDFQTNRADGSSTGISKQQAEQNRVIANKILVQYYKEFQERNPNLAVYNAVIHNDEISP
                     HLHLNIVPVAEGYKRGVQKQPSFNKALVQQGIHADKDNGRVLFNNFRNQEVDSIERLMN
                     DYGWKRDIVGTNKIKDIHEYKEIMSEISELRQTAVKERESVSAEMRYIYRQREENEREK
                     ALVASERAEIEEEKKNMLNVKKEMAVIFQKDMVPLESFKRLPDGSYHLSGNDFVDLYQR
                     ATRATNAKRNADNMSEQYLQMLEQNTELNEYVAALEEERHLSGRKQLADLQVENKKLKE
                     ENRSLRQRLERLKNAFQKSITRLSIRFGLAEKDMGLSEELEVLEQEKTLFYRQNVSQHK
                     LERSEDEIEW"
                     /name="plasmid recombination protein"
     gene            complement(1323..1685)
                     /locus_tag="HI845_RS15145"
                     /old_locus_tag="H4J14_015140"
     CDS             complement(1323..1685)
                     /locus_tag="HI845_RS15145"
                     /old_locus_tag="H4J14_015140"
                     /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_098379973.1"
                     /translation="MGVTLADIKAQEEKLKKEQAKLRQQKKRLIEKENAEMGKALRKHF
                     GFESFADFERWLSSISDDQQHEKSVDNEWLADEKSAPSERDYLNESDGLFEVIPNNKSQ
                     MSESKFTSMFSDVDLR"
                     /name="hypothetical protein"
     gene            complement(1738..1986)
                     /locus_tag="HI845_RS15150"
                     /old_locus_tag="H4J14_015145"
     CDS             complement(1738..1986)
                     /locus_tag="HI845_RS15150"
                     /old_locus_tag="H4J14_015145"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002323248.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002323248.1"
                     /translation="MKLDKQRLYEAVKDNCNCGGNRQLFKAMMVTVYRRLDGENAETAV
                     ENAYFQVFGEHHSPEWDRAILDDMAEMHEKLWRALND"
                     /name="hypothetical protein"
     gene            complement(1973..2953)
                     /locus_tag="HI845_RS15155"
                     /old_locus_tag="H4J14_015150"
     CDS             complement(1973..2953)
                     /locus_tag="HI845_RS15155"
                     /old_locus_tag="H4J14_015150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002355134.1"
                     /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_002299242.1"
                     /translation="MAKKKQDLINGTFREKKRNLKKIMAFGDGRISGKTLENMKACGSF
                     MEFIATVDKEKKKMVHGMFCKNRFCPVCAYRKARKDSYMLSIMMEAIQAEKGYEYIFMT
                     LTTPNVPADKLSEEIDRFNKALSKLFRRKRVMTSIKGYVRKLEITYNKSRNDYNPHFHL
                     IMAVNKSYFTDKRYYIAQAEWLDMWRDVTGLDGINEDGTDEICSLDVRKVNGYRQEKAV
                     SEIAKYSAKDFEMTYSQDVFDTFYFAMKGRQLMTFNGVFKEYRKKYDAGELDHYRQKDE
                     NDYFWFLTASWMQKDANYSVAVRELTDDEKKFFAERYDKEGDETG"
                     /name="protein rep"
     Typing          complement(1974..2947)
                     /name="rep_cluster_1077"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.692"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(8..1194)
                     /name="MOBV"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.152"
                     /coverage="98.0"
                     /evalue="0.0"
ORIGIN
        1 ttctgtattt tgctcaagca tctgtaaata ttgctcactc atgttatcag catttctctt
       61 ggcatttgtt gctctcgtag ctcgttgata caaatcaaca aaatcattcc cagataaatg
      121 atacgaacca tcaggaagcc tcttgaaact ttctaaagga accatatctt tttggaaaat
      181 gaccgccatc tcttttttta cattcagcat atttttcttc tcttcttcaa tctccgctct
      241 ctcagaagcc accagagcct tctcacgctc gttttcttct ctttgcctat aaatatacct
      301 catttccgca gaaacgctct cacgctcttt tacagccgtt tggcgcaatt cagaaatttc
      361 actcatgatt tctttgtatt cgtgaatatc tttaattttg ttggtaccga caatatccct
      421 tttccaaccg taatcattca ttaatcgttc tatagagtca acttcttgat ttctaaaatt
      481 attgaaaagc actcgaccat tatctttatc agcgtgtatc ccttgttgaa ccagtgcttt
      541 attaaagctc ggctgctttt gaacaccccg tttataacct tcagcaaccg gcacaatatt
      601 caagtgcagg tgcggactta tttcgtcatt atgaataaca gcattataaa cagccaaatt
      661 agggtttctc tcttgaaact ccttgtaata ctgaaccaaa attttattgg caatcactcg
      721 attttgttca gcttgttgtt tcgatatgcc agtagaagaa ccatctgctc gatttgtctg
      781 gaaatcatct aaaatgccta tttgcacaat aaattctcgt tgaggttcca actttttatc
      841 cttgcgcact ttcgctaaat agtcctcgat ttttctatcg gctctttttt gtttcgcatt
      901 atatttttct accacttcgc caaacaattc ctcatattta tctgctagat tcgtctgctc
      961 taaataaata ttttcatccg atttcgtgaa gtcaatgtgc ttatgccaat cattggtttt
     1021 ctggcgatca gttaactcac gattattatg agaaatactt gtattcttcg ttcctttttt
     1081 aaatgaaata ctaaacccca agttaaaacc ctccttcgcg ctgtcgctaa taaaaagagt
     1141 gtaaaccttt ctgttactct ttgtcaaaga gtaacatttt cctaattgtg acatggctgt
     1201 cacaattcca aatgctctcc gagggtattc gctgtcacaa gtgacaacga aaaaaggagc
     1261 cgaaagcgtg tcacgctctc aactcctttt acgctttatt ttgcttcacg caaaataatc
     1321 gcttatcgta aatccacgtc actaaacatt gacgtaaatt tactctcact catctgactt
     1381 ttattattcg gtatcacttc gaataagccg tcagattcgt ttagataatc tcgttcgctt
     1441 ggcgctgatt tttcatcagc aagccactca ttatccactg atttttcgtg ttgctgatcg
     1501 tcagaaatcg acgatagcca ccgctcaaaa tcagcaaaag attcaaaccc aaaatgcttg
     1561 cgaagcgcct tgcccatttc agcattttcc ttctcaatca atcgcttttt ctgttggcga
     1621 agttttgcct gctctttttt caatttttct tcttgtgctt taatatcagc taaagttact
     1681 cccatgaatt acaactcctt acccttagat tcattcctat aaataacacc aatttgatta
     1741 gtcatttagc gccctccaca atttctcgtg catttccgcc atatcatcaa gaatagcacg
     1801 atcccattca gggctatggt gttcaccgaa cacttgaaaa taagcatttt ccacagctgt
     1861 ctcagcattt tccccatcca accgacgata aacagtcacc atcatagcct taaaaagctg
     1921 acgatttccg ccacaattac aattatcttt caccgcttca tatagccttt gcttatccag
     1981 tttcatcacc ctccttatca tagcgttccg caaagaattt cttctcatca tccgtcaact
     2041 cacgaacggc caccgagtaa ttggcatcct tttgcatcca gctagcagtc aagaaccaga
     2101 aatagtcgtt ttcatctttc tggcggtaat gatccagctc accggcatcg tattttttcc
     2161 tgtactcctt gaacacgcca ttgaaagtca tcagctgacg acctttcata gcaaaataga
     2221 acgtgtcaaa aacgtcttgg gaataagtca tttcaaaatc tttggcagaa tatttagcaa
     2281 tttccgatac cgccttttct tgccggtacc cattgacctt gcggacatcc aacgaacaaa
     2341 tttcgtcggt accgtcctca tttatgccat ccaaaccggt gacatcccgc cacatatcca
     2401 gccattcagc ttgggcaata taatagcgtt tatcagtaaa atatgattta ttaacagcca
     2461 taatcaagtg aaaatgcggg ttataatcat ttcggctttt gttatacgtt atctccaatt
     2521 ttcggacata gcccttgatt gaagtcatca ccctttttcg acgaaatagc ttcgacagtg
     2581 ctttgttgaa acgatcaatt tcttcggata atttgtccgc cggcacgtta ggcgtggtga
     2641 gtgtcataaa gatatattca tagccctttt cagcttgaat agcttccatc atgatagaca
     2701 acatatagct gtctttacgg gcttttcggt atgcacaaac cggacaaaac cggtttttac
     2761 agaacatgcc atgaaccatc tttttcttct ccttatcaac cgttgctatg aactccatga
     2821 atgatccaca ggctttcatg ttttccaagg ttttgccaga aatacgacca tcaccaaatg
     2881 ccatgatttt ctttaaattt ctcttttttt ctcggaaagt gccattgatc aaatcttgct
     2941 ttttcttcgc catatgctat actgaacctt gcagaacaca aacgttccgc ccaaacattt
     3001 aaaaaacgca ttttctaaat gcacgaaaaa aaggttgcac tcctctcttg ttttatgact
     3061 attgacttag acactcaaag catacaacac taggtacgga tatgcaactt ttttttgttt
     3121 aaaaccctta taggtcaagg gaaaaacaca tacataggac ccgattttct gccgaaaata
     3181 gttaccctat gtatcaagat aagaaaaaac atcaaaaaaa gagggcgaaa atcgccccct
     3241 ttttttcgtt ttaaaacccc aaaacccaaa ggcataaatt tcggtcaatt gaccactgaa
     3301 tttttagggg ggtgtccata aaagggacac ttaaccgcct gttagagggg gctgttaatt
     3361 tttcccactc attcttagtc atgcaaacat aaaaccgcac cctttaaaaa gggcgccccc
     3421 aaacttcgct aacgctaagt tggccaaaaa atggacttgc cattttttag caaatgtcag
     3481 cttcagggat tagtggttta gccgtcaact ccttatcctc ggcacaaacc gcctccggta
     3541 ccgttgactg cacatcgtaa ctaccactcg atctcatctt cagaacgctc taatttatgc
     3601 tgtgagacgt tttgacgata aaataaggtt ttctcctgct ctaatacttc taattcctca
     3661 gaaagcccca tatccttttc tgcaagccca aaacggatag acaaacgagt gatcgatttt
     3721 tgaaatgcgt tttttaatcg ctctaaacgc tggcgtaaag agcgattttc ttctttcagc
     3781 tttttatttt ccacttgtaa atctgctaat tgttttctac cagacaaatg acgctcttct
     3841 tccaatgcag ctacatactc atttaa
//
