LOCUS       NZ_CP059770             4464 bp    DNA     circular CON 20-SEP-2023
DEFINITION  Enterococcus faecium strain A11051 plasmid pA11051_P6, complete
            sequence.
ACCESSION   NZ_CP059770
VERSION     NZ_CP059770.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14675381
            Assembly: GCF_012933285.2
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4464)
  AUTHORS   Veerarghavan,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  JOURNAL   Unpublished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 4464)
  AUTHORS   Veerarghavan,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 4464)
  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                     :: A11051
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 91.28x
            Sequencing Technology :: Illumina HiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/20/2023 03:44:53
            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)                     :: 3,089
            CDSs (total)                      :: 2,997
            Genes (coding)                    :: 2,835
            CDSs (with protein)               :: 2,835
            Genes (RNA)                       :: 92
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 70
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 162
            CDSs (without protein)            :: 162
            Pseudo Genes (ambiguous residues) :: 0 of 162
            Pseudo Genes (frameshifted)       :: 51 of 162
            Pseudo Genes (incomplete)         :: 102 of 162
            Pseudo Genes (internal stop)      :: 36 of 162
            Pseudo Genes (multiple problems)  :: 25 of 162
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP059770.1.
            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..4464
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="A11051"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pA11051_P6"
                     /geo_loc_name="India: Vellore"
                     /lat_lon="12.9165 N 79.1325 E"
                     /collection_date="2019"
                     /collected_by="CMC Vellore"
     gene            join(3993..4464,1..452)
                     /locus_tag="HI861_RS15320"
                     /old_locus_tag="HI861_015320"
     CDS             join(3993..4464,1..452)
                     /locus_tag="HI861_RS15320"
                     /old_locus_tag="HI861_015320"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002296860.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_002351085.1"
                     /translation="MANEIVKYENRLNHIPLRKFNSREMNLFFSIASRVREKGVDEIIF
                     SFHDLKKLSGYTERGEQFIKDLSSTYDKLLSINAWNDDGNTLTKFVAFTKYSIIRDKQL
                     VIISVNPEFKGLFNQLKNWTRFNLEQFTNLDSTYSKTMFRLLKQYRTQGWTEFSKEKFF
                     DLLDIPKSYWNSPSNIDKFILRPIKEELTPLFKGLTIRKKYGKGRGKPVIGYRFTWKAE
                     INHADDFSKGKQEDLRIKLFNIDHNGELTREEKWRAKDRILNLPLGTHEADFKQQQQTE
                     EKQAEKRELSNKLKQDLLGNLQNLFD"
                     /name="replication initiation protein"
     gene            468..1007
                     /locus_tag="HI861_RS15325"
                     /old_locus_tag="HI861_015325"
     CDS             468..1007
                     /locus_tag="HI861_RS15325"
                     /old_locus_tag="HI861_015325"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016616811.1"
                     /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="WP_002351084.1"
                     /translation="MADKTIKELAEELGVSKTAINKKVSDKNRKLWFAKNGNKFVINET
                     GQKAIKSMFLVDNANLNRKLVGEKSKTKNHKNTNQVSELKLLSFLEKQLNRKDIQLQEK
                     DNQIKQMQKLLDQQQQLTLQANQQIENLQEQLHLTYTEETPTTESTAFSEKKADNTQPL
                     IEKKWWQIWKSNRTNL"
                     /name="DUF536 domain-containing protein"
     gene            1692..1865
                     /locus_tag="HI861_RS15330"
                     /old_locus_tag="HI861_015330"
     CDS             1692..1865
                     /locus_tag="HI861_RS15330"
                     /old_locus_tag="HI861_015330"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002341717.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_162897362.1"
                     /translation="MLKKTVLVLGSISLGILGFSPMLLSVIGKNNSNRELKLNSNYYNS
                     PNEELFVKQTDK"
                     /name="hypothetical protein"
     gene            2269..2703
                     /gene="bacA"
                     /locus_tag="HI861_RS15335"
                     /old_locus_tag="HI861_015335"
     CDS             2269..2703
                     /gene="bacA"
                     /locus_tag="HI861_RS15335"
                     /old_locus_tag="HI861_015335"
                     /inference="COORDINATES: protein motif:HMM:NF041453.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bacteriocin 51 precursor BacA"
                     /protein_id="WP_002351079.1"
                     /translation="MKNKIIKIITCLFLFGMIVGASTPLNLFPFSARGIKVEAASSRYN
                     HNHRGFTCYKMNYYVTNKMCRDLKKNYNKLKTPAQIASFIPIGGVGTWVITNAFSSAVD
                     AMNVFVRAANQGKGVQLTYNAHFSNTTSYQYNDYARYVIK"
                     /name="bacA"
     Typing          2..452
                     /name="rep_cluster_1291"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccaaagaaaa attttttgat ttactagata ttcctaaaag ttattggaat agtccgtcaa
       61 atattgacaa atttatctta aggccaatta aagaagaact cactccctta tttaaaggat
      121 taactattcg taaaaaatat ggtaaaggtc gaggtaaacc tgttatcggt tatcgtttta
      181 cttggaaagc tgaaattaac catgctgacg atttttccaa agggaaacaa gaagatttac
      241 gtataaaatt atttaatatt gatcacaatg gagaattaac acgagaagaa aaatggcgcg
      301 ctaaagatcg aatactaaat cttcccttag gcactcatga agctgatttt aaacaacaac
      361 aacaaactga agaaaaacag gcagaaaaac gagaactttc aaacaaactc aaacaagatt
      421 tactaggaaa tttacaaaac ttattcgatt aagcttaagg agtatttatg gcagataaaa
      481 caatcaaaga acttgcggaa gaattaggag ttagtaaaac agcaattaac aaaaaagttt
      541 ctgacaaaaa tcgaaaactt tggtttgcaa aaaacggaaa caagtttgtg attaacgaaa
      601 ccggtcaaaa agctataaaa tcaatgtttt tagtcgataa cgcaaactta aatcgaaaac
      661 tagttggcga aaaatcaaaa accaaaaacc ataaaaacac caaccaagtt tccgaattaa
      721 aactcctttc tttcctagaa aaacagttaa atcgaaaaga tatacagcta caagaaaaag
      781 ataatcaaat aaaacaaatg caaaaattac tcgaccagca acaacaactc actctacaag
      841 cgaaccaaca aattgagaac ctacaagaac agctccattt aacttataca gaagaaactc
      901 caacaaccga atcaactgcc ttttctgaaa aaaaagcaga caatacacaa ccacttattg
      961 aaaaaaagtg gtggcaaatt tggaaatcta atagaaccaa tctctaaaat tttctagaag
     1021 ttagttcgga tagtagagga aaaagttgta ctacctgatg gggagatcac tcaaattttt
     1081 atgagaaaga aaaaatagtt tacaactgta aacaatcaat gtttatagtt gtaaactatc
     1141 aaactatatg gtgacttatt gcttaaaata ggttgaaatc tcactcaatt tttggtggaa
     1201 aaacaaaata aattctaatc gattttgttg aaaaagtcat aaaaaaacaa atgtgatttt
     1261 aacaaaattt caaaaaaatc gtttgaaatt tcgtttattt tttttgagaa ttttgatcat
     1321 cgtagggtca ttgtagaatc attatgagat catcgtggga tcatcgaata aagtatggga
     1381 aaggcttgcg gtgcttggta ttaagggcat tctccgcctc ccaggttctt gaccattttc
     1441 tctcaacgtg gtaaaaatcc cacttataag agaaaatggt caagaaccta aacggtcggc
     1501 gaagaaaaca taccaagcac cacaagcaaa aaaagttaga gtaacttcca aaaaagaaaa
     1561 attttttaga acaacttttg aaaatttaat tttgatttat atccgttcaa tttaaacatt
     1621 tgataaactg aaggctagta tttaaaatgt gtatacaagt ggtagcgtta aaaaaagtgg
     1681 aggtataacc tatgttaaaa aaaactgtgt tggtactggg ttctatttct ctaggaatat
     1741 taggttttag ccccatgcta ttatccgtaa ttggaaaaaa caattccaac agagaactta
     1801 aattaaattc aaattattac aacagtccta acgaagaatt gtttgtaaaa caaacggata
     1861 aataataaaa aagactgctc tttcgagcag ccagttaaaa aataatgagt gtttattctt
     1921 gaaaaagcac gcgcttatga agcgctacca aaaatttacc atattttaca aaaaataaca
     1981 agtcttaaaa aaatgacaga taaaaatgca caaagaatta gatatagata accgcgaaaa
     2041 atcaagcttt agaaagttgc ttttagctag accaatgaaa aatcacaaag tgagcgtctc
     2101 tatccattgg tagaggggct acttggcata ctcgacatta tgtctactaa cctttaaaat
     2161 aacacgtttt ataaaataaa ccctcttgac aatatttaat tttctgatta ttctaaatat
     2221 atacagaaag cgctttccta ggattttata tctaaggagg aagtaacaat gaaaaataaa
     2281 attattaaaa ttattacttg tctatttttg ttcggtatga ttgttggagc aagtactccg
     2341 ttaaatctgt ttccttttag tgctagaggt ataaaagtgg aagctgcaag ttcacgatat
     2401 aatcataatc atcgtggatt tacttgctat aaaatgaact attatgttac taataaaatg
     2461 tgtagagatt tgaaaaaaaa ttataataag ctaaagactc ctgctcaaat tgcatctttt
     2521 attcctattg gtggagttgg aacatgggtt attacaaatg cttttagtag tgctgttgat
     2581 gcaatgaatg tctttgtaag agctgcaaat caaggaaaag gtgtacaatt aacatataat
     2641 gctcacttta gcaatacaac atcatatcaa tacaatgatt acgctcgtta tgtaataaaa
     2701 taatcagaaa gtgaaactat ctcatgaata aaaagatttt agctgtaatt atttcaataa
     2761 tagttttaat cactatgttc ttcatattta ggctaatttt caatataagc ttacaaaaaa
     2821 gtattcttta tctaattcct atagcattta tcttagcaat ttttagaagt atttacggaa
     2881 ataaaaactc taaatagcta aaaataaatc atactaaatt ttacaaaaag tggctagcat
     2941 tttctagcca ctttttgtat tgtggagcgt gggttttgag ggggattcaa gggggagctt
     3001 gcgccccttt gacaagcggt tatttgcacc aaatacggag gtatttggct agcaaatata
     3061 gagcttgcca aaccctttta gtgagttttg tagaaagtac ctttaaaggt actttcacat
     3121 tacgaacgat acgtccgtag gacgtactga aagggtggga cttatgagca aattaatgca
     3181 aaatttggct agcaaaaaag ctaaaaaata tatgctaata atcgagcgaa ataaacactt
     3241 tttcaagtga gcgaatccgc catgacaaag ctgaagcagt ttatttcagc tttgtcatgg
     3301 cgtgtgccga cttttttaaa agtctaggca cacgagcaaa tatctttatc aagctctaat
     3361 ttgcgtttta agacgtttga aacgcctaag tatataaata tataagaata ggtttaagag
     3421 tgcttaaatc gaattttaga gggcatttag acaattttag ggttgttagg gcttgccctg
     3481 accgcctgta aggcgtttta agaacaagat aagggattta tactaggact gtcttaaaat
     3541 gtcttaaacg aacgctcaga gcttctcaaa gggttcctta tgaacggctt ttagcaaagg
     3601 agccggaggc gactgcgcag tataatgtga gagcagagcg atcacacctt tttagcgaac
     3661 cgtagggagc aaggtttgga attggcagtt ttgataaatt cgcgaacctg tttagagaaa
     3721 aaaggagtga ttttttaggc gggaaaatta gcctcccctc tttttatatc tctttttata
     3781 tctcttttta tatctctttt atgtcggctg tgtccttact ctcccaagca attcagagtt
     3841 ttttcaagta ggttttctac gcttttcaag taggttttct acgcttttca agtaggtttt
     3901 ctacgctttt caagtaggtt ttccgacatt attgagtatt tttataaagt atgttacttt
     3961 tatttcatac tttataaaag taggagaagc ttatggcaaa tgaaattgta aaatatgaaa
     4021 atagattaaa tcatattcct ctgagaaaat ttaatagtcg tgaaatgaac ttattttttt
     4081 caattgcttc acgtgtacgt gaaaaaggtg tagatgagat tattttttca tttcacgatt
     4141 tgaaaaaact aagcggttat acagaacgtg gggaacaatt tataaaagat cttagtagca
     4201 cgtatgacaa attattaagt attaatgctt ggaatgatga tggaaatact ttaactaaat
     4261 ttgttgcttt cacaaaatat agcattatac gagataaaca acttgttata atttcagtta
     4321 atccagaatt taaaggactt tttaatcaat taaagaactg gacaagattt aatctagagc
     4381 aatttactaa tttggatagc acatattcaa aaactatgtt tcgattatta aaacaatatc
     4441 gaactcaagg ctggactgaa tttt
//
