LOCUS       NZ_CP071963             6262 bp    DNA     circular CON 22-APR-2024
DEFINITION  Enterococcus faecium strain VB13828 plasmid p5VB13828, complete
            sequence.
ACCESSION   NZ_CP071963
VERSION     NZ_CP071963.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18353823
            Assembly: GCF_017603725.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 6262)
  AUTHORS   Balaji,V., Yamuna,B.D. and Anushree,A.
  TITLE     Complete genome of vancomycin resistant E. faecium_VB13828
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6262)
  AUTHORS   Balaji,V., Yamuna,B.D. and Anushree,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (19-MAR-2021) Clinical Microbiology, Christian Medical
            College, Ida Scudder Road, Vellore, Tamil Nadu 632004, India
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2021
            Assembly Method :: CANU v. v.1.7; UNICYCLER HYBRID v. v.0.4.6
            Assembly Name                     :: VB13828
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 59.0x
            Sequencing Technology :: Illumina HiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_017603725.1-RS_2024_04_22
            Annotation Date                   :: 04/22/2024 04:36:32
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 3,107
            CDSs (total)                      :: 3,015
            Genes (coding)                    :: 2,851
            CDSs (with protein)               :: 2,851
            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)              :: 164
            CDSs (without protein)            :: 164
            Pseudo Genes (ambiguous residues) :: 0 of 164
            Pseudo Genes (frameshifted)       :: 52 of 164
            Pseudo Genes (incomplete)         :: 102 of 164
            Pseudo Genes (internal stop)      :: 38 of 164
            Pseudo Genes (multiple problems)  :: 26 of 164
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP071963.1.
            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..6262
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="VB13828"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p5VB13828"
                     /geo_loc_name="India"
                     /lat_lon="12.9165 N 79.1325 E"
                     /collection_date="2020"
                     /collected_by="Christian medical college"
     gene            complement(join(6161..6262,1..864))
                     /locus_tag="J4767_RS15270"
                     /old_locus_tag="J4767_15270"
     CDS             complement(join(6161..6262,1..864))
                     /locus_tag="J4767_RS15270"
                     /old_locus_tag="J4767_15270"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_169043415.1"
                     /translation="MATIKLARTTSCNRAISYAEKRAVEKDGLNCEISNAKQEMTTVRE
                     LYSKNDKTQAHLCIQSFNPEESQRLGAKKINQLGIELAEKIAPNHQVAVYTHADKAHIH
                     NHIVINAVNLETGKKYHHNNDFDRVSRLHDDLLKEHKLEIVQKQAIERRTMAERQLKQK
                     GKAVWKDTIRQKIDTLMKDSSVRSYKAFRERLEEKGIKVHERGKNVTYELLESNKRVRG
                     TKLGTDYEKERIKNELDRRERNQKLAPNEQRYQRFKERLADGQSENRTHSPNRRPISDR
                     ERLAELRHERELAEQSRLAERNIPDVKPTIPKNIDFGPKL"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(846..1229)
                     /gene="mobC"
                     /locus_tag="J4767_RS15275"
                     /old_locus_tag="J4767_15275"
     CDS             complement(846..1229)
                     /gene="mobC"
                     /locus_tag="J4767_RS15275"
                     /old_locus_tag="J4767_15275"
                     /inference="COORDINATES: protein motif:HMM:NF017524.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_098388130.1"
                     /translation="MPDKNYRINKRKEKSNRTYTQVNFRLTETEKKKWQSHADQLHMTL
                     PKFTKYIMNGFFELGYIKQPKIDKQQGAEIAKNLGRLGGNVNQIAKWCNTHKDTISDEQ
                     AQRLADNLEQVQKELKKAWQQLN"
                     /name="mobC"
     gene            complement(2104..2754)
                     /locus_tag="J4767_RS15280"
                     /old_locus_tag="J4767_15280"
     CDS             complement(2104..2754)
                     /locus_tag="J4767_RS15280"
                     /old_locus_tag="J4767_15280"
                     /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_169043416.1"
                     /translation="MNNKKTIRDLANELNIERKKVKNKVDYLKRNGEISADIQSGVIYL
                     SEADQITVCKSLNVPIFYANSADSQLPVNQLKEQVEDLKSDKEFLKKRIEEQERANSEL
                     RILLEKSIKQNEQPSLAENMSKKPQIENAETIYNKEINRFSGVAEKPTEKSYEEMTEEE
                     KFWELNPNYKSYWNERLRPLREGKLDRQSFKVAKLRARRLKKTLEKIEKKKFF"
                     /name="hypothetical protein"
     gene            complement(2744..3712)
                     /locus_tag="J4767_RS15285"
                     /old_locus_tag="J4767_15285"
     CDS             complement(2744..3712)
                     /locus_tag="J4767_RS15285"
                     /old_locus_tag="J4767_15285"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016127586.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA cytosine methyltransferase"
                     /protein_id="WP_169043417.1"
                     /translation="MLKIASFFAGVGGIDLGFENAGFKTIYANEFDNYAADTFEMNFDV
                     KVDRRDINDVQADEIPDFDIMLAGFPCQAFSIAGYRQGFNDEQGRGNLFFELVRILEAK
                     KPRVAFFENVKNLVSHDSGNTFRVICSELERLGYKYLFQVLNASEYGNIPQNRERIYIV
                     AFKNKKDYANFELPKSIPLKTTIHDVIDFSKKQDDKFYYTSEKNKFFDDLKENMTNHDT
                     TYQWRRVYVRENKSNLVPTLTANMGTGGHNVPLILTYSGEIRKLTPRECFNVQGFPKEY
                     KLPNQSNGRLYKQAGNSVVVPVIERIALNIFDTLYGNKYEQ"
                     /name="DNA cytosine methyltransferase"
     gene            complement(3818..4390)
                     /locus_tag="J4767_RS15290"
                     /old_locus_tag="J4767_15290"
     CDS             complement(3818..4390)
                     /locus_tag="J4767_RS15290"
                     /old_locus_tag="J4767_15290"
                     /EC_number="3.1.21.-"
                     /inference="COORDINATES: protein motif:HMM:NF021052.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Bsp6I family type II restriction endonuclease"
                     /protein_id="WP_169043418.1"
                     /translation="MEIKQLQGDLLAYKKFGYIEIDDARIDATCDAYFKWKDLNTYIKN
                     TSSRGMNIPDAISEPMGCYCLGYLWNRGSEVGDATDPITNKKIEFKATSKFEGDLSSFG
                     PKTVFDNLVFLRFYLDENKLYIYDLNINSEEFGKYPANRTQTIQEQKAVGRRPHVSLQS
                     LFVDAKNLQPDIIFDIRRCRIIEDNRH"
                     /name="Bsp6I family type II restriction endonuclease"
     gene            complement(4434..5249)
                     /locus_tag="J4767_RS15295"
                     /old_locus_tag="J4767_15295"
     CDS             complement(4434..5249)
                     /locus_tag="J4767_RS15295"
                     /old_locus_tag="J4767_15295"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002415063.1"
                     /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_143458265.1"
                     /translation="MAKKQNYIWKNDRNFALDEYEQQKYYYVAESNDLITKARHDLDAR
                     ELKIMDYVVSKIKPDDEDFNIVQTSMYELTNVLNLKRNGRTYSQLAESLESMRAKSVRV
                     YSEVEKRLTLTGWFEVVDLWENGKVQLKINKQFAPYLLQLKHDYTQHLLIDTVKLKSKY
                     SILLYKLMREADKDKGKSIAILQGTPEDFKEWLGAPEDYEYKDLKRNILKKAVEEINLK
                     IEDMDLEILQGRYGRKVAQVEIHNNWTVQRATKENAEYVESITTHDWLN"
                     /name="replication initiation protein"
     gene            complement(5890..6210)
                     /locus_tag="J4767_RS15300"
                     /old_locus_tag="J4767_15300"
     CDS             complement(5890..6210)
                     /locus_tag="J4767_RS15300"
                     /old_locus_tag="J4767_15300"
                     /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_208572930.1"
                     /translation="MLNQLSQRISTLDQSSKHYEKQVLGIVRWKTLAKQFLELLLYLGA
                     IVLLVHALTTSLWQTIGLKALYEHFNGQKNIQLGLTIAYIAIVLGLFVWVLRKVVKSSR
                     YY"
                     /name="hypothetical protein"
     Typing          complement(4438..5269)
                     /name="rep_cluster_2229"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.249"
                     /coverage="97.0"
                     /evalue="0.0"
ORIGIN
        1 tcgaagttca gcaagtcgtt ctcggtcact aattggtcga cggtttgggc tatgagttcg
       61 attttctgac tgtccgtcag caagtcgttc tttgaatctt tggtatcttt gttcgtttgg
      121 tgcaagtttt tggtttcttt ctcgtctgtc caactcattt tttatcctct ctttttcata
      181 atctgttcct aatttcgttc cacgaaccct cttattactc tctaaaagct cgtaggtgac
      241 gttttttcct ctttcgtgta cttttatacc tttttcttct aaacgctccc taaacgcctt
      301 atatgatctt acagagctat ctttcatcaa agtatcaatt ttttgtctga ttgtatcttt
      361 ccaaacggct ttgccttttt gttttagctg acgttctgcc attgttcgcc gttcgattgc
      421 ttgtttttga acgatttcta gtttgtgttc tttcagcaag tcatcgtgca agcgagaaac
      481 acggtcaaaa tcgttgttat ggtggtactt ctttcctgtt tctaaattca cggcgttaat
      541 cacgatatgg ttatgaatat gcgctttgtc cgcatgggta tagacagcga cttggtgatt
      601 aggtgcgatt ttttcagcca actctatccc taactgattg atttttttgg caccaaggcg
      661 ttggctttct tccggattaa aagactgaat gcaaaggtgc gcttgtgtct tatcgttttt
      721 tgaatacagt tctctaacag tcgtcatttc ctgcttggca ttactaattt cgcaattcaa
      781 accgtctttt tcaacggctc gtttttcggc ataactaatc gctcgattac agcttgttgt
      841 acgtgctagt ttaattgttg ccatgccttt ttcaactcct tttgaacctg ttctaagttg
      901 tcagctaagc gttgggcttg ttcgtctgaa atggtgtctt tatgcgtatt gcaccacttc
      961 gcaatttgat tgacgtttcc tcctaatcgt cctaaatttt tcgctatttc cgccccttgt
     1021 tgtttgtcaa ttttgggttg cttaatatac ccaagttcaa aaaaaccatt catgatatat
     1081 tttgtaaatt taggcaaggt catgtgcaac tgatcggcat gcgattgcca tttctttttt
     1141 tccgtttccg tcaaacgaaa attcacttgc gtataggtgc ggttgctttt ttctttgcgc
     1201 ttgttgattc gatagttttt atctggcatg gaacataccc ccttccattc tcaaagtcgg
     1261 ctatccgccg atttgttcat tcacttgtct tttgagttgt ctattcgaca atcgaaagac
     1321 aagcagacag agaaaactcc ttattcagtc gtttcccttt gtctgttttt gtgcctacgg
     1381 ctacaaaaag gtcaaaagat agcgaaagta aatttccctc ttcggtcaat ttcctttcgc
     1441 tattctctag ttttagttgt tcgttattca ctcgcaactt gcacaagaga atacgtcaaa
     1501 ctgttcccta tgcggttaca gttttccttt aagttttgta atctccttgc tcgctatcca
     1561 ctcacaactc aataacaaaa cacgcaccct cattatagca taataagggt ttggcaagca
     1621 gtccaaatgc tagcacttcg tgctacattt gcgcttgtcg gggagattcc ccgaaccccc
     1681 gttttcgcca gaaaaaagta agctgttcgc ttatttttcc aacgaaaact aaaaccctat
     1741 gcaaggaaat agtcgggagc atccgcctat ttctcttgtt tttctcgctt gctcgaaaaa
     1801 gctccgccgg tgatttcatc aagactcttt cagagggtcc acttcgtgga gactgctccg
     1861 cagagtgctt gtcagcagga ctgcctactc ggcaagagca agtgtagcac gcttgaccgc
     1921 tataaaaacc tattatttat gctgtttatt taacagactt aatcccccca agaaatccaa
     1981 taccttttaa tatacctaaa ggtaaatttt tattactaat ctaaataaca ttcccaaagg
     2041 aatacctgtt gcaatccagt tattgttgtt attgtttatt tttattttgc tgcccctttt
     2101 attctaaaaa aactttttct tctcgatttt ctctagcgtt ttctttaatc tgcgggctct
     2161 tagctttgcg actttaaaag attgcctgtc caattttcct tctcttagag ggcgtaatcg
     2221 ttcattccag taactcttat agtttggatt taattcccaa aatttttctt cttccgtcat
     2281 ttcttcataa cttttttcag ttggtttttc cgctacacct gaaaaacggt taatttcttt
     2341 gttataaatg gtttcagcgt tttcgatttg tggcttttta gacatatttt ccgctagtga
     2401 aggttgttca ttttgcttga ttgatttttc gagcaagata cgtaattcag agttagctct
     2461 ctcttgttct tctattcgtt ttttgagaaa ttctttatct gattttaggt cttccacttg
     2521 ttcttttagt tgattgactg gtagctgaga atcagctgaa tttgcataaa aaataggcac
     2581 gttcaaagac ttacaaaccg ttatttggtc tgcttctgat aggtagataa ctcctgactg
     2641 aatatcagct gaaatctcgc catttctttt tagataatct accttgtttt taactttttt
     2701 tctttcgata tttaattcat tagcaagatc tctaatggtt tttttattgt tcatatttat
     2761 taccatacaa tgtatcaaat atatttaagg ctattctctc aattactggt actacaacac
     2821 tgtttcctgc ttgtttatat aatctcccat tactttggtt tggaagttta tattcttttg
     2881 ggaaaccttg aacgttaaag cattctcttg gtgttaattt acgaatttct ccgctatatg
     2941 taaggattag aggcacatta tgcccacctg ttcccatatt agccgttagt gttggtacta
     3001 aattactttt gttttctctt acataaactc tgcgccactg atatgtagtg tcgtgattag
     3061 tcatattttc ttttaaatca tcaaaaaatt tattcttttc agaggtatag tagaacttat
     3121 cgtcttgttt tttagaaaaa tcaataacat cgtgaatcgt tgtttttaaa ggtatagatt
     3181 ttggtagttc aaaatttgca taatcttttt tatttttgaa agcaacaata tagatacgtt
     3241 ctctattttg aggtatattt ccatattcag aagcattaag cacttgaaaa agatacttgt
     3301 accctagtct ttctaactca gaacaaataa ctctaaatgt gttcccgcta tcgtgagaaa
     3361 caagattttt aacattttca aagaatgcaa cacgaggttt ttttgcttct aaaatacgaa
     3421 caagttcaaa aaaaagatta cctctacctt gttcatcgtt aaagccttga cgataaccag
     3481 caatagaaaa ggcttggcaa ggaaaacctg ctaacataat atcaaaatct ggtatttcat
     3541 cagcttgtac atcatttata tcacgtcggt ctaccttaac gtcaaagttc atttcaaaag
     3601 tatcagcagc ataattatca aattcattag catatattgt tttgaaacct gcattttcaa
     3661 aacctaaatc aattccgcca actccggcga aaaaagaagc aattttcaac ataaatattc
     3721 tcctataaat caagtatgat atatagtata caaaaaaaag cggcacgccg caattttaat
     3781 atgctgaata gggagataaa acaactcccc tttcagttta gtgtctatta tcttcgataa
     3841 ttcgacatcg tctaatatca aaaataatat ctggttgtaa gttttttgcg tctacaaaca
     3901 aagattgtaa actcacgtga ggacgccttc caacagcttt ttgttcttgt atagtttgag
     3961 tcctatttgc tggatatttc ccaaactctt ctgaattaat gtttaaatca taaatatata
     4021 atttattttc atccagataa aatctcagaa atactaaatt atcaaagact gttttaggtc
     4081 cgaaagaaga taaatcccct tcaaactttg atgttgcctt aaactcaatt tttttatttg
     4141 tgattgggtc tgttgcatca ccgacttcac tgcccctatt ccatagatat cctaagcaat
     4201 aacaccccat aggttcacta attgcatcag ggatattcat tcctcgagaa ctagtgtttt
     4261 taatataggt gtttaggtct ttccatttaa agtaggcatc acaagttgca tctattctgg
     4321 catcatcaat ttcaatatat ccaaactttt tataagccaa taaatcacct tggagttgtt
     4381 ttatctccat gattttattt taacaaaaat tagttcccgt aactaacatt tatttaattc
     4441 aaccaatcat gagtcgtgat actttcaaca tattccgcat tttctttggt tgctcgctgt
     4501 acagtccaat tgttatgaat ttcaacttgt gcgactttac gaccgtatct cccttgtaaa
     4561 atttctaagt ccatatcttc gatttttaga ttaatttctt caactgcttt tttaagaatg
     4621 tttcttttta agtctttata ttcataatct tctggagcgc ctagccactc tttaaaatct
     4681 tcgggcgttc cttgtaatat agcaattgat ttccctttat ccttatcagc ttctcgcatc
     4741 agcttgtaaa gcaaaataga atatttactt tttagtttta cagtatctat caataaatgc
     4801 tgtgtatagt catgttttaa ttggagaaga taaggagcga attgcttgtt aatcttcaat
     4861 tgaactttcc cattttccca aagatcaaca acttcaaacc agcctgttaa cgttaaacgt
     4921 ttttcaactt cgctatatac acgaacgctt ttagctctca tagattccag actttcagct
     4981 agttgactat atgttcgtcc attcctcttt aaatttaaaa cattagttag ttcgtacata
     5041 gaagtttgaa caatattaaa gtcttcatcg tctggtttaa ttttcgatac cacataatcc
     5101 atgattttta attctcttgc gtctaaatcg tgtcttgcct tagtgattaa gtcattagat
     5161 tctgccacat aatagtattt ttgttgttca tattcatcta atgcaaagtt acggtcattt
     5221 ttccaaatat aattttgttt ttttgccata atttttatcc tttcaaacaa acagttaaag
     5281 agtataaaga gattatatca taaaagtgac accaactcct ctttttatat aaaatactca
     5341 ccagtcgtgt gctttttact caccagtcgt gtgcttttta ctcaccagtc gtgtgctttt
     5401 tactcaccag tcgtgtgctt tttactcacc tattacgccc gcaaacgttg atataaaggc
     5461 attctcattt ccctaagtat tataaagtat taaagaatta taaaggaaat ataaaagcgc
     5521 gcgtaggcgt gtgttttgtt tttctattct aagaacaaac aacacaagac aaaaaataaa
     5581 aaaaggagtg agcgaaagac acgctcacat taaacttgca gcgttcactt tcgttcactc
     5641 gctaaggtca aaatcaaaag acggttggtc aaggtcgggt tggggtagtg ctaaaacggc
     5701 atataagcgt ttctaagacg ttcttagtgg tttcagctaa tcttgttcat caggcgcctt
     5761 tcaggcggtc agggcaagcc ctaacaacca aaagcggtta gaatagcgag aacatgaaat
     5821 gttcttgttg ttctaactgc catcatcggt ctgctcgatg acaggagcag tcagcttgaa
     5881 aagctgaaac taataatacc tagatgattt cactactttt cgtaagaccc acacgaaaag
     5941 acctaaaaca attgctatat aagcaattgt aagccctaat tgaatatttt tttgaccgtt
     6001 gaaatgttca tacaaggctt tcaaaccgat tgtttgccag agagaagtcg tcaacgcatg
     6061 aacgagtagg acaattgccc caagatacaa gagtaattca agaaactgtt ttgctaaggt
     6121 tttccaacga acaatgccta gcacttgttt ttcatagtgt ttagagcttt ggtccaaagt
     6181 cgatattctt tgggatagtt ggtttaacat ctggtatgtt tctttctgca agtcttgact
     6241 gttctgcaag ttctctctca tg
//
