LOCUS       NZ_CP059753             4991 bp    DNA     circular CON 03-OCT-2023
DEFINITION  Enterococcus faecium strain A7214 plasmid pA7214_P6, complete
            sequence.
ACCESSION   NZ_CP059753
VERSION     NZ_CP059753.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14675388
            Assembly: GCF_012933165.2
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4991)
  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  JOURNAL   Unpublished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 4991)
  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 4991)
  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                     :: A7214
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 95.82x
            Sequencing Technology :: Illumina HiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/03/2023 03:40:33
            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)                     :: 3,080
            CDSs (total)                      :: 2,987
            Genes (coding)                    :: 2,866
            CDSs (with protein)               :: 2,866
            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)              :: 121
            CDSs (without protein)            :: 121
            Pseudo Genes (ambiguous residues) :: 0 of 121
            Pseudo Genes (frameshifted)       :: 48 of 121
            Pseudo Genes (incomplete)         :: 68 of 121
            Pseudo Genes (internal stop)      :: 33 of 121
            Pseudo Genes (multiple problems)  :: 24 of 121
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP059753.1.
            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..4991
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="A7214"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pA7214_P6"
                     /geo_loc_name="India: Vellore"
                     /lat_lon="12.9165 N 79.1325 E"
                     /collection_date="2019"
                     /collected_by="CMC Vellore"
     gene            complement(join(4984..4991,1..397))
                     /locus_tag="HI844_RS15190"
                     /old_locus_tag="H4J16_015190"
     CDS             complement(join(4984..4991,1..397))
                     /locus_tag="HI844_RS15190"
                     /old_locus_tag="H4J16_015190"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016529521.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF2251 domain-containing protein"
                     /protein_id="WP_008321396.1"
                     /translation="MTILVTIQAQLVVGEEQVIKSLAPEGMLAAVFEDDGRTGYFYALD
                     ESVEGNPIMDAVHIYNAEDVSDGHIPSDVKIGWSEDSQKCVLLINGYPHGAFDFVGKNG
                     YCRSGYPPPINKVWSLSGHEWSDSVDDFFR"
                     /name="DUF2251 domain-containing protein"
     gene            complement(1192..1593)
                     /locus_tag="HI844_RS15195"
                     /old_locus_tag="H4J16_015195"
     CDS             complement(1192..1593)
                     /locus_tag="HI844_RS15195"
                     /old_locus_tag="H4J16_015195"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009310048.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_012579088.1"
                     /translation="MARVSISEAARLTGKSRTTLHRLIKAGDLSTCSGERNAKMVDTSE
                     LLRVFGPFEQPKGEHHSGQVSGQRDTASADQSEQVIRHLKQEIEHLNTLLLSKDSHIDS
                     LKQAMLLLENHQAKLTESPAPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(1593..1784)
                     /locus_tag="HI844_RS15200"
                     /old_locus_tag="H4J16_015200"
     CDS             complement(1593..1784)
                     /locus_tag="HI844_RS15200"
                     /old_locus_tag="H4J16_015200"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_004187666.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDVEADLCEKLHDDA
                     EHLFRTLSSRLDALQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2200..2366
                     /locus_tag="HI844_RS15660"
                     /pseudo=""
     CDS             2200..2366
                     /locus_tag="HI844_RS15660"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505258.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            2696..3754
                     /locus_tag="HI844_RS15205"
                     /old_locus_tag="H4J16_015205"
     CDS             2696..3754
                     /locus_tag="HI844_RS15205"
                     /old_locus_tag="H4J16_015205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012508929.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ParA family protein"
                     /protein_id="WP_042109829.1"
                     /translation="MAIYAVWNNKGGVGKSYLTFQLASEYARQNPTKKVLVVDLCPQAN
                     SSSMLLGGMINGENTLNQIHSAIQRKTISGYIEDRIRSPYIPTNTGSSYVINVSTHNSK
                     VPNNLYLVTGDEQLELQASRVVGASFPGPHDAWRTVHLWINDLISDICNSWNNEDSCVF
                     IDCNPSFSIYTELALTAAERLLIPFSADGSSKRAVKAVLSLVYGERRHQNEPQSDFYLN
                     SNRYSMSLPQIYMYVGNRLTQMNNSSASAFKTVVTEIGDEIWKVWQTKPSLFCIHPNGS
                     STPNNKRSFRNMFQYEVNDANTASVVSGALGIPIATLTAGNKTVSGKIIKVNQTQLDKQ
                     VPNIVALAGMIE"
                     /name="ParA family protein"
     gene            complement(3784..4041)
                     /locus_tag="HI844_RS15210"
                     /old_locus_tag="H4J16_015210"
     CDS             complement(3784..4041)
                     /locus_tag="HI844_RS15210"
                     /old_locus_tag="H4J16_015210"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_042109830.1"
                     /translation="MGSNNNQNKDLQDKQADLLDQTYTLGWMDGYAEGYDDAIEDTQNA
                     LNKLENENELLTEVVESKDNVIKELASSAGRALQAVKKNK"
                     /name="hypothetical protein"
     gene            4459..4890
                     /locus_tag="HI844_RS15215"
                     /old_locus_tag="H4J16_015215"
     CDS             4459..4890
                     /locus_tag="HI844_RS15215"
                     /old_locus_tag="H4J16_015215"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001025244.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF6530 family protein"
                     /protein_id="WP_042109831.1"
                     /translation="MKIPAHLKHKPIIQVENYDRIDGPHADDTDAMGLSVGIAQWNTPG
                     WTELSAKVWRNTGEKWSRQSEELPLHRVIDLATLICITMDYSKNGRLSSSDDFPVTRST
                     DNPELAHHTEFMKKELKQNKSNLDVSLKRLSTELKRLGY"
                     /name="DUF6530 family protein"
     Typing          1906..2308
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.365"
                     /coverage="99.0"
                     /evalue="1.6700000000000002e-161"
ORIGIN
        1 aaaaatcatc cacagagtcg ctccactcat gcccggaaag agaccacacc ttgtttatag
       61 ggggaggata accactcctg cagtacccgt tttttcccac gaaatcgaat gccccgtgcg
      121 ggtatccatt gatcaggagt acgcacttct gactgtcttc tgaccagcca attttaacat
      181 cagaaggaat gtgaccgtct gaaacgtctt cggcattgta gatgtgtact gcgtccataa
      241 tcgggtttcc ctcgacggac tcatcgagcg catagaaata cccggtccgg ccatcgtctt
      301 cgaacacggc ggccagcatg ccctcaggag cgaggctctt tataacctgt tcctccccga
      361 caacgagctg ggcctgtatc gtcactaaaa tggtcatcag gtctgttctc ctttccttgg
      421 ttgcttcggc agccagcttt cagacaagcg gataatttac cataacatcc gttatcagca
      481 tcgtcagaaa cgcgctgagg gcgtttctga cgggaaaccg gtaaaacagg caacaaacca
      541 cccgaaaacc cgccagaaac gcgcaggctc tgtttttacg gcatgcatga gtatgcacgc
      601 aagtgcatag cgcgaatatt cacgccattc agacagggta agtcctgttt ccggcgttct
      661 tcccatccga aaacggtgaa cggggacgca atttattgcg tggccgtgaa gcgttgccgg
      721 cgcagccgga aaaccggttt tcagcacgtt caggaatcgg gttcgtcgac ggccggcaat
      781 cacgttatgg caagtcgccg gacgactcac cacacgattc accggcgact ctgcactaga
      841 gtcgtaccta gagtcgccgc gactaaaaaa caaccaaacg gggagtcggg tctagagtcg
      901 ggtcgttatt aactcattgt ttttatagcc ctgagtcgtt accgactcta tgacgactcg
      961 ccggggactc tatgacgagt cgtcatagag tcggatctat ataaataaaa tttaaaaaac
     1021 gaaatctcag gaaagtaaac tactgatatt aaatacaaat ctgcaaaatt ttaattttgc
     1081 gtggggtgtg ggtattttta gtggtgagga gcgttcagag atctgacgat ttttgggaag
     1141 gttcaggaac tccccgggat ggccggagag gaaaactgaa gcatgacagg gtcaggattt
     1201 tttccagaat ttccaccatg gcgccgggga ttcagttaat tttgcctggt gattttcaag
     1261 aaggagcatg gcctgtttca ggctgtcaat gtgcgaatcc ttggacaaaa gtaaggtgtt
     1321 caggtgttca atctcctgtt tcagatgacg gatcacctgt tcactctggt cagcagaggc
     1381 tgtatcacgc tgtccagaga cctgtccaga atggtgttca cccttcggtt gctcaaaggg
     1441 gccaaagaca cgtaaaagct ctgaagtatc taccattttt gcattgcgct caccgctaca
     1501 ggtggacagg tcacctgctt taattaacct gtgcagtgtt gttctactct tacccgtcag
     1561 tcgggcagcc tcactaatag acactctggc catcagttac catcctgtaa tgcatccagt
     1621 ctcgaggaca gtgtacggaa aagatgctcc gcatcatcgt ggagtttctc acaaaggtcg
     1681 gcctcgacat cgagatcaag ctcgttaagc ttctccagca ggagcagaga ctgattctgg
     1741 atgaatttag ccatgttcag cgctgttttc tgttgtttcg tcataagagg cctcagagcg
     1801 tcagtggtca gtgtagggat ctcctctttt ccgcttcctc gctcactcag tcgctacgct
     1861 cctgccgttc ggctgcggcg agcggcagga gcatgcgtag aaacgctcga gaaaaccgag
     1921 taatcgcatg gaggaaagaa ggaaaggccg cacagcggcc gtttttccat aggctccgcc
     1981 cccctgacga gcatcacgga atctgacgct caaatcagtg gtggcgaaac ccgacaggac
     2041 tataaagata ccaggcgttt ccccctgatg gctccctcgt gcgctctcct gttcctgcct
     2101 ttcggtttac cggtgtcatt ccgctgttat ggccgcgttt gtctcattcc acgcctgaca
     2161 ctcagttccg ggtaggcagt tcgctccaag ctggactgta tgcacgaacc ccccgttcag
     2221 tccgactgct gcgcctgttc cggtaacttt cgacttgagt ccaacccgga aggcacgaca
     2281 aaacgccact ggcagcagcc actggtaagg ggtgtacaag aattactggt gcagagttct
     2341 tgaagttaca gcctaactac agctaaactg aaaggacaga tttggtggca gcggtcttgt
     2401 acaccctgtt accacggttc agaagttccc caacttactg atccttcgaa aaaccacctc
     2461 cccaggtggt tttttcgttt acagagcaaa agattacatc ccgcaggtta ggatctcaag
     2521 aagatccttt taatcggaat tcgacaactc cagataagtc atggtgagcc agccaacccc
     2581 ttcgactgaa tatcgttcca aaaaaaggca gtcagctgaa agaaactaac agtagaacaa
     2641 taatctctag taccctgaat ctaagctaac aacaaaacta gattaggagt tatagatggc
     2701 gatctatgcc gtatggaata acaagggtgg tgtagggaaa agttacctta cttttcagtt
     2761 agcctctgaa tatgccagac agaaccctac taaaaaggtc ctggtggttg acctgtgccc
     2821 acaagcgaac tcgtcctcta tgttacttgg tggaatgata aatggcgaaa acacactaaa
     2881 ccagattcat tcagcaatac agagaaagac aatatctgga tatattgagg ataggatcag
     2941 aagtccatat attcctacca acactggttc tagctatgta ataaatgtat ctacacacaa
     3001 tagtaaagtt ccaaataatc tatatcttgt cactggcgat gaacaattag aactccaagc
     3061 atcaagagtt gttggggcat catttccagg tccccatgat gcatggcgta ctgttcacct
     3121 ctggattaat gatttaatca gtgacatttg caactcatgg aataatgaag atagctgcgt
     3181 attcattgac tgcaacccta gcttctctat ttatacagag ttagctttaa ccgcagcaga
     3241 gcgcctttta attcctttct ctgccgatgg ttcatcaaag agagcagtta aggctgtact
     3301 ttctttagtt tatggtgagc gtcgccatca gaatgaacca caatcagatt tctatcttaa
     3361 tagcaatcgt tattctatgt cgctaccaca aatatatatg tatgttggaa atagattaac
     3421 gcaaatgaac aattcatctg ccagtgcatt taagacggta gtaaccgaaa ttggtgatga
     3481 aatttggaaa gtatggcaaa caaaaccaag tctgttttgt attcacccaa atgggagctc
     3541 aacgccaaat aataaaagat ctttcaggaa tatgtttcag tatgaagtaa atgatgcaaa
     3601 cacagcatct gtcgtatctg gagccttagg tattccaatc gcgacattaa ctgcaggaaa
     3661 taaaactgtt tcaggaaaaa taataaaggt taatcagacg cagctagata aacaagtccc
     3721 caacattgta gctctcgctg gtatgatcga ataaaatagc aaggccctta aaagggcctt
     3781 tttttatttg tttttcttta ctgcttgcag cgccctgcca gcactagagg ccaactcttt
     3841 gattacatta tctttacttt caacaacctc agtaagcaac tcgttttcgt tttccagttt
     3901 attcaaagcg ttctgagtat cttcaatagc atcatcatac ccttcggcat agccatccat
     3961 ccaaccaaga gtatacgttt ggtccaaaag atcagcttgc ttatcctgca gatctttatt
     4021 ctgattattg ttagagccca tgttttttcc tcatttgttg gcgcatctga gttttcaaac
     4081 caggaggaat tccatttcta agtttctcac ttagtctgac tggtggtgtg tttcctgaga
     4141 ctggattaca gtcagcatcc accccgacat ctttcttttt atagtcgcca atattcctaa
     4201 cgttatctgt agtcatagaa aaccacgccc attgctgtga ataaccgaac tataaaccag
     4261 aaaaaaaacg tacggcttat cataacactt gacacaaaaa aacaccgcta ctctccaagc
     4321 aaaaaacata aaattggaaa aacaaaatca caagcacatg ataacaatag atattaatat
     4381 ttacttacat ttagtgagtt ttataattag aaaaacaatg taatttaata atcacaaaca
     4441 ttacctaagg acgaactgat gaaaataccc gcgcatttga agcataaacc aattattcaa
     4501 gtcgaaaatt acgaccgcat tgacggccca catgccgatg acactgatgc tatggggcta
     4561 tctgtaggta ttgctcaatg gaacactcct ggatggactg agctttcggc aaaggtttgg
     4621 cgaaacacag gagaaaaatg gtcaagacaa tcagaagagc tgcctcttca ccgggtaatc
     4681 gaccttgcaa ctctgatctg tatcaccatg gactacagta aaaatgggcg actttcatcc
     4741 agtgatgatt ttcccgtgac tcgctcaact gataaccctg agctagcaca tcacactgag
     4801 tttatgaaaa aagagttaaa acaaaataaa agcaatcttg atgtaagcct caaacgcctc
     4861 tcgactgaat tgaagagact tggctattaa aactagcttt agaaatgtct acctacttca
     4921 cagacgaatt taccataaca tccgtttttc gaaccataat ggcaggctat agcctgccgt
     4981 aattcaccgg a
//
