LOCUS       NZ_CP059779             6096 bp    DNA     circular CON 06-NOV-2023
DEFINITION  Enterococcus faecium strain A3895 plasmid pA3895_P7, complete
            sequence.
ACCESSION   NZ_CP059779
VERSION     NZ_CP059779.1
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 6096)
  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  JOURNAL   Unpublished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 6096)
  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 6096)
  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
            CP059779.1.
            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..6096
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="A3895"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pA3895_P7"
                     /geo_loc_name="India: Vellore"
                     /lat_lon="12.9165 N 79.1325 E"
                     /collection_date="2019"
                     /collected_by="CMC Vellore"
     gene            join(6066..6096,1..173)
                     /locus_tag="HI845_RS15070"
                     /old_locus_tag="H4J14_015065"
     CDS             join(6066..6096,1..173)
                     /locus_tag="HI845_RS15070"
                     /old_locus_tag="H4J14_015065"
                     /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="WP_002321382.1"
                     /translation="MFLISKSLKSLKTFTKKNPQIATIRIFIFAIAVAIIVNMLSGGQL
                     YKSGLFLVLILVVLDIIKSKKK"
                     /name="hypothetical protein"
     gene            496..876
                     /locus_tag="HI845_RS15075"
                     /old_locus_tag="H4J14_015070"
     CDS             496..876
                     /locus_tag="HI845_RS15075"
                     /old_locus_tag="H4J14_015070"
                     /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="WP_189660794.1"
                     /translation="MSEQNQNLASDPSKKYTYRSEPKQISFRVSESEFAKLKQSAEALQ
                     MSVPAFVKAKAQNARLVTPKVAPDIAQAIARDLAKAGGNINQIAKWCNTHQHDVAPDDA
                     QRLSENLKIMQKELQKIWQQLK"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            858..1796
                     /locus_tag="HI845_RS15080"
                     /old_locus_tag="H4J14_015075"
     CDS             858..1796
                     /locus_tag="HI845_RS15080"
                     /old_locus_tag="H4J14_015075"
                     /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/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_104858995.1"
                     /translation="MATVKVSRTTSCSRAINYAEPRATVKTGINCDIDYAKSEMKQIRM
                     LYGKDDHVQAHLLIQSFRPGEITAEKANQLGKEYAEKIAPEHQIAIYTHTDKDHIHNHI
                     VINSVNLETGKKFQAHGQAFLDKCYDINDEICLTHGLSITERGKKEEKRTMSEIKLKEK
                     NEPVWKDEIRFAIDQTMKNPKTRTYDQFCDSLKIFGIHCFNRGKNFTYELIKKKKKVRS
                     NKLGKDYEKETILHELDRREQTYYRERERAYHRQQADELRRARESIRKIAGEVRREQRT
                     FTPEQSEIRSTRRNHEQHVERGTDHQQELSL"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            2036..2725
                     /locus_tag="HI845_RS15085"
                     /old_locus_tag="H4J14_015080"
     CDS             2036..2725
                     /locus_tag="HI845_RS15085"
                     /old_locus_tag="H4J14_015080"
                     /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="WP_125276269.1"
                     /translation="MAFYLPYLLIFVSISGSIWLSCKIYQTRHSLKGSKIRFKRFLLLG
                     CIFSLIIISSGLFGILEGNKRISGSILLENVTQKYEVARDKKKKEQALAQKIEEFTACY
                     ENMNDIFVKQEKRLTDKNMETLTRLYRKLPEKQQKEYQEKYEQVKKDVQYVKDTQTEEA
                     CYDLFSDTIPFSTSEQERKERQQSVTYERYEILLQKATNIQNPTKKETALNYLESVKEW
                     LDQQQQN"
                     /name="hypothetical protein"
     gene            3576..4313
                     /locus_tag="HI845_RS15090"
                     /old_locus_tag="H4J14_015085"
     CDS             3576..4313
                     /locus_tag="HI845_RS15090"
                     /old_locus_tag="H4J14_015085"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015060391.1"
                     /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_002292475.1"
                     /translation="MSNDIVRYNNGLNSVPLRKFTPIDMDLFWGICSKMKRKGTKEEIF
                     TFKQIKELIDYNINARGDRFANDLIKMSKKIITLSFIYEDEKTYEQLNLFQKFKIDKVN
                     ETLLIKVSEEFEYILNSIGTNFTRFELENMTNLKSSYVKELYRQLMAHKNRRSKKGHWF
                     VKIEDFRALLAIPESYRMRDIDKQIFAQAKKEFLNVNSTHPAIFKTFEIKKIKAYKGNK
                     IGSLQIYFEENIPSITLDNWLEK"
                     /name="replication initiation protein"
     gene            4341..4874
                     /locus_tag="HI845_RS15095"
                     /old_locus_tag="H4J14_015090"
     CDS             4341..4874
                     /locus_tag="HI845_RS15095"
                     /old_locus_tag="H4J14_015090"
                     /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="WP_104858994.1"
                     /translation="MQPKETFTIKELSELFEISRQAISKHVDKLDPSLLAKNDRGYKVV
                     LRSGVLQLARNLGNQRLLDKLHEHEQNSDKNAYIPTKNVVANELLDQLREENKFLREQI
                     ALKEQNNSHIQKLLDQQQQLTLQANQQIDKLQKRLQLVYTEETSENESTTLSEETESIE
                     KQTKKKQKWWKLWK"
                     /name="DUF536 domain-containing protein"
     gene            4890..5060
                     /locus_tag="HI845_RS15100"
                     /old_locus_tag="H4J14_015095"
     CDS             4890..5060
                     /locus_tag="HI845_RS15100"
                     /old_locus_tag="H4J14_015095"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002322958.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002322958.1"
                     /translation="MTRKKLIFGSILLGILGFSPMLLSVINKGNKHGELKLNPNYYNSP
                     NEELFVKETDK"
                     /name="hypothetical protein"
     gene            5521..6054
                     /locus_tag="HI845_RS15105"
                     /old_locus_tag="H4J14_015100"
     CDS             5521..6054
                     /locus_tag="HI845_RS15105"
                     /old_locus_tag="H4J14_015100"
                     /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="WP_002334266.1"
                     /translation="MKKFTLGVALLTIGAVVLPSTTIVYASENSQVVSLNENNATENVV
                     IEYTEDGMVVTKYEDGYSAEDFANSSDIMTRAAVARWGKKEYTNIAVTTGVAANAINAA
                     FWAGGKASTSMFGIPGWAIGALLTGASWTKKGASPGNAVAKEWDKNGNGWIGFYYQRGY
                     DAAGRVVATRYSTL"
                     /name="hypothetical protein"
     Typing          3577..4313
                     /name="rep_cluster_1742"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          859..1793
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.705"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 taaaaacatt tactaaaaag aatccgcaaa tagctactat tcgtattttt atatttgcta
       61 tagctgttgc tataattgtt aatatgctaa gcggagggca attatacaaa tctggtttat
      121 ttttagtgtt aatcttagtt gtcttagaca taataaagtc taaaaaaaaa taaatcgata
      181 cattttagaa gaatagggtt gtttgaatat tacaaagcaa caatttcacc ttcggtgaaa
      241 taagcgaaac tttacaaaaa gtggctagca aatgctagcc tttttttgta ttgtggagcg
      301 tggattttga gggggattca agggggagct tgcgctcctt tgacaagcgg ttatttgcac
      361 caaatacgta ggtatttggc tagcaaatat agagcttgcc aaaccctttt agtgagcttt
      421 actcattgta cctttttagg tataatgagt attgcgaacg atacgtccgt aggacgtact
      481 gaaagggtgg gacttatgag cgaacaaaat caaaatttgg ctagcgatcc ttctaaaaaa
      541 tatacctatc gatccgagcc aaaacaaatc agttttcgag tgagcgaatc cgaatttgca
      601 aagctgaagc agtcagctga agctttgcaa atgagtgtgc cggctttcgt gaaagccaag
      661 gcacaaaacg cgcgtctggt gacaccgaaa gtggcgccag acattgccca ggcaatcgcg
      721 cgcgatttag ccaaagctgg agggaatatc aatcaaattg ccaagtggtg caatacacac
      781 caacacgacg ttgctcctga tgatgctcaa cgtttgtccg aaaacctaaa aatcatgcaa
      841 aaggagctac aaaagatatg gcaacagtta aagtaagtcg aaccacttca tgtagccgag
      901 caatcaatta cgcagaacca cgagcaaccg tcaaaacagg aataaactgt gacattgatt
      961 atgccaaaag tgaaatgaaa caaatacgta tgctttacgg aaaagacgat catgtacaag
     1021 cacacttatt gattcagtcc tttcgaccag gagaaattac cgccgaaaaa gccaaccagc
     1081 taggaaaaga atacgctgaa aaaatcgcac cagaacacca aatcgcgatt tatacgcaca
     1141 cggacaaaga ccatatccac aatcacattg tcattaattc ggtcaattta gaaacaggaa
     1201 aaaagtttca agcacatggt caagcattcc tagataagtg ttacgatatc aacgacgaaa
     1261 tttgtttgac tcatggttta agtatcactg aacgaggaaa aaaagaagaa aaacgaacta
     1321 tgtctgaaat caaactaaaa gaaaaaaatg aacctgtttg gaaagacgaa attcgctttg
     1381 ccattgatca aaccatgaaa aatccaaaaa ccagaaccta tgaccaattt tgtgattccc
     1441 tcaaaatatt tgggattcat tgcttcaatc gtgggaaaaa ttttacttac gaattaatca
     1501 aaaaaaagaa aaaagtacga tccaacaaat taggaaagga ctatgaaaag gagacaattt
     1561 tacatgagct ggacagacga gaacaaacct attatcgaga acgagaacga gcctatcata
     1621 gacagcaagc cgacgagctt cgaagagctc gagaaagcat tcggaaaatt gctggagaag
     1681 tacgaagaga acaacgaact tttacgcctg aacaatcgga aattagatcg actcgaagaa
     1741 accatgaaca acacgttgaa cgaggaacag accaccaaca agaattatcg ctctaaaacg
     1801 ttaaaagaca tagaaaacga aataaaaaga caacgtgctt ttcttgcgcc ttatacccaa
     1861 gaaaggatac aaactacaat tgattcacaa gtcaaaaaac tccaccaagc gctattagac
     1921 cagcgaaacc aagaacaaaa aaaggcttta attcaacgat cgatggatat tcttgccccc
     1981 ttatgttgct tagtcctgac actgttcgca ttttggttag tatggggagg ctaaaatggc
     2041 attttattta ccctatctac tcatttttgt tagtatttca ggaagtattt ggctcagttg
     2101 taaaatttat caaacaagac attcattgaa aggctctaaa attcgattta agcgattttt
     2161 attgcttggc tgtatatttt cattgataat catttcaagt ggcttattcg gcattttaga
     2221 gggaaataag cgcatttcag gaagtatttt attagaaaat gtcactcaaa agtatgaagt
     2281 agcacgtgat aaaaagaaaa aagagcaagc attagcacaa aaaattgaag aatttaccgc
     2341 ttgttatgaa aacatgaatg atatttttgt gaagcaagaa aagcgattga cggataaaaa
     2401 tatggaaaca ctcactcgtc tttatcggaa attgccagaa aaacagcaaa aagagtacca
     2461 agaaaaatat gaacaagtaa aaaaagacgt gcaatatgtg aaagatacgc aaacagaaga
     2521 agcgtgttat gacttattca gtgatacaat ccctttttca actagcgaac aagaacgaaa
     2581 agaacgacaa caatcagtca catatgaacg ctatgaaatc ttgcttcaaa aggcaactaa
     2641 catacaaaat ccaacgaaaa aagaaacagc attaaattat ctagaaagtg tcaaagaatg
     2701 gctggatcag caacagcaaa attgaatttg attgaaactc atgttaaact aaatatgcaa
     2761 ataggtaatc ataagataca cgaaagtcct agagaagtcg gattctctag gacttttttt
     2821 gtaggctgat atcgccttag ttgattttac ttcttgtttc ggttattcag ccaataacta
     2881 aataaagagt ttagaagctc aacaagaagg gcgcaaataa agtgggtaat cataagatac
     2941 acctccttcc agtcgcaaga ctgtcggata ggcgacaagt tattatatct taaaaaatta
     3001 aatctgtgtg gtgtttttaa gtatccctta ttttagggtt gttagggctt gccctgaccg
     3061 cctgtaaggc gctttaggaa ctgataaggt tttcccctag aactgtctca aaacggttta
     3121 gacgagggct cagagcccca caaggttctc tttgaacaac ggttttggca aaggagcctt
     3181 taggcgactg cgcagtacaa tgtgagagca tagcgatcac acctttttag cgaccgtagg
     3241 gagcaagttt tccagtttag aaaaattcgc gaacctgttt gagtaaaagg tagtagtttt
     3301 ttaggcggga aattaaatgt gctcttaaga tatactgtta gatatactgt tagatatact
     3361 gttaataata actgttaggt attagcaacc tcatgggaga gtaagtattg acataggtag
     3421 tgggggataa attgtcacac tatgggggat aaattgtcac actatggggg ataaattgtc
     3481 acactatggg ggataaattg tcacactatg ggggataaat tgtattttac atcctcttat
     3541 gtctatgata acataattta ttgaggtgat ttttattgag taacgatata gttcgatata
     3601 ataatggatt aaattctgtc cctttaagaa aatttactcc tatagatatg gatttatttt
     3661 ggggaatatg ttctaaaatg aaaagaaaag gtacaaaaga agaaattttt acatttaaac
     3721 aaataaaaga attaattgat tacaatataa atgcacgtgg cgaccgtttt gctaatgatt
     3781 taataaaaat gtcaaaaaaa atcattactt tgtcttttat ttatgaagac gaaaaaacat
     3841 atgagcaatt aaatctgttt caaaaattta aaatcgataa agtgaatgaa acattattaa
     3901 taaaggtttc tgaagaattt gaatatatac ttaattcaat cggaactaat tttactcgtt
     3961 tcgaattaga aaatatgaca aacttaaaga gtagctacgt taaagagtta tatcgccaac
     4021 ttatggctca taaaaacaga agatctaaaa aaggtcactg gtttgtaaaa atagaagatt
     4081 ttagagctct attagcaata ccagaaagtt atcgcatgag agatattgat aaacaaattt
     4141 ttgcccaagc gaaaaaagaa tttttaaacg ttaattcaac tcaccctgct atttttaaaa
     4201 cttttgaaat caaaaaaatt aaagcctaca aaggaaataa gataggatct ctgcaaattt
     4261 attttgaaga aaatatacct tcaattacct tagataattg gttagagaaa taatacctaa
     4321 caatttagga ggcaattatc atgcaaccca aagaaacctt tacaataaag gaattatctg
     4381 aattatttga aataagtagg caagcaatct ctaaacatgt tgataaatta gacccgtcct
     4441 tattagctaa aaatgatcgt ggttataagg ttgtattacg ttctggagta ttgcaacttg
     4501 ctcgcaattt aggcaaccaa aggttgctag ataagttgca tgaacatgaa caaaacagcg
     4561 ataaaaatgc ttatatacca acaaaaaacg tggttgcaaa tgagttgctc gatcagttgc
     4621 gtgaagaaaa taaattttta cgtgaacaaa tcgctctcaa agaacaaaat aattctcata
     4681 tacaaaaact cttagaccag caacaacaac tcaccttgca ggcaaatcaa caaatcgata
     4741 aactgcaaaa acggttacaa ttagtttata cggaagaaac ttcagaaaat gaatcaacta
     4801 ctctttctga agaaacagaa tcgatagaaa aacaaacaaa gaagaagcaa aaatggtgga
     4861 aactatggaa ataactggag gaaacattca tgacaagaaa aaagctcata tttggttcta
     4921 ttttactagg aattctaggc ttcagtccga tgttattgtc agtgatcaat aaaggaaata
     4981 aacatggtga attgaaattg aatccaaatt attacaacag tcctaacgaa gagttatttg
     5041 taaaagaaac ggataaataa taaaaaaaga ctgctcttcc gagcagccca aaatgaaatt
     5101 atcctattca tcaacataaa aatattacaa aatgaagaac tagaagaagg acaaaaaaag
     5161 catatcaaat cctctaaaaa ataacaagtc tttaaaaagt gaccggtaaa aatgcacaaa
     5221 gaactaaaaa agagaaattg catcaaatca agcattagaa gctagtaact agctagacca
     5281 attgaaaatc acaaagtgag cgcctgtatc gattgctaca ggcgctactt ggcatagtgt
     5341 acattatgtc aacaagaatt taatataaca tattttccta atgcattcta actataccac
     5401 attatcaaaa atataaatta tctttactaa ataaaatatt gacaagccta taccttttgt
     5461 tttatgattt tcacaaagaa aacgttttct atatattttt ctgtatcagg aggaaattct
     5521 atgaaaaaat ttactttagg ggtagctttg ttaactattg gggcagttgt tttaccgtca
     5581 actactatag tttatgcttc agaaaattcc caagtggtat cattaaacga aaacaatgct
     5641 actgaaaatg tagttattga gtacactgaa gatggtatgg tcgtaactaa atatgaggat
     5701 ggttatagtg cggaagattt tgcaaattct tcagatatca tgacaagagc tgcagttgca
     5761 agatggggca aaaaggaata tacaaatatt gctgtaacca ctggagtagc tgctaatgct
     5821 attaatgctg ccttttgggc aggagggaaa gctagcactt ctatgtttgg tatcccaggt
     5881 tgggcaattg gtgctttgtt aacaggtgca agttggacta aaaaaggtgc ttctccaggg
     5941 aatgcagttg caaaagaatg ggacaaaaat ggtaatggct ggattggatt ttattaccaa
     6001 aggggatatg atgcagctgg aagagttgta gctactagat attcaacgtt ataagttaag
     6061 gagtgatgtt tttgatatct aaatcattaa aatcat
//
