LOCUS       NZ_CP016168             4796 bp    DNA     circular CON 22-APR-2024
DEFINITION  Enterococcus faecium strain ISMMS_VRE_11 plasmid ISMMS_VRE11_p5,
            complete sequence.
ACCESSION   NZ_CP016168
VERSION     NZ_CP016168.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN03988630
            Assembly: GCF_001721905.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 4796)
  AUTHORS   Bashir,A., Attie,O., Sullivan,M., Sebra,R., Singh,K.V., Altman,D.,
            Pak,T., Dutta,J., Chacko,K., Webster,E., Lewis,M., Hamula,C., Delli
            Carpini,K.W., Murray,B.E., Kasarskis,A., van Bakel,H. and
            Huprikar,S.
  TITLE     Genomic confirmation of vancomycin-resistant Enterococcus
            transmission from deceased donor to liver transplant recipient
  JOURNAL   PLoS One 12 (3), e0170449 (2017)
   PUBMED   28301471
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 4796)
  AUTHORS   Bashir,A., Attie,O., Sebra,R., Singh,K.V., Altman,D., Pak,T.,
            Lewis,M., Dutta,J., Hamula,C., Delli Carpini,K.W., Murray,B.E.,
            Kasarskis,A., van Bakel,H. and Huprikar,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-JUN-2016) Genetics and Genomic Sciences, Mount Sinai
            School of Medicine, 1425 Madison Avenue, New York, New York 10029,
            USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. May-2014
            Genome Coverage                   :: 38.0x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_001721905.1-RS_2024_04_22
            Annotation Date                   :: 04/22/2024 02:03:03
            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)                     :: 3,111
            CDSs (total)                      :: 3,018
            Genes (coding)                    :: 2,815
            CDSs (with protein)               :: 2,815
            Genes (RNA)                       :: 93
            rRNAs                             :: 6, 5, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 5, 6 (5S, 16S, 23S)
            tRNAs                             :: 72
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 203
            CDSs (without protein)            :: 203
            Pseudo Genes (ambiguous residues) :: 0 of 203
            Pseudo Genes (frameshifted)       :: 132 of 203
            Pseudo Genes (incomplete)         :: 69 of 203
            Pseudo Genes (internal stop)      :: 30 of 203
            Pseudo Genes (multiple problems)  :: 24 of 203
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP016168.1.
            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..4796
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="ISMMS_VRE_11"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="ISMMS_VRE11_p5"
                     /geo_loc_name="USA: New York City"
                     /lat_lon="40.7127 N 74.0059 W"
                     /collection_date="2011-05-24"
                     /collected_by="Shirish Huprikar"
     gene            complement(join(4295..4796,1..323))
                     /locus_tag="AL025_RS17035"
     CDS             complement(join(4295..4796,1..323))
                     /locus_tag="AL025_RS17035"
                     /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_227003440.1"
                     /translation="MIYKLKKLHQELLDQRNKEQKKGAYSTIIGFSCPLMLLSPDTVRI
                     LVSMGRLKWHFILPYLLIFVSISGSIWLIYKIFQTRYSLKGSKIRFKRFFFSWLYIFLD
                     NRFNHYTNNKNSKYQLKLPNNFLNINIYPFSHVENIGLSEILYVQGNSNKLIPVLKKYG
                     TPTISNINQSDTFQINTNIVLVICYLSIFIVITTIIFAFSKMKEITLKKMLGYNSFDTI
                     KDSIKELNLLFCSLIITFILSIFLSIYYSNENFFLSFLLCSIFHFIISFYLS"
                     /name="hypothetical protein"
     gene            complement(408..1322)
                     /locus_tag="AL025_RS16205"
                     /old_locus_tag="AL025_15435"
     CDS             complement(408..1322)
                     /locus_tag="AL025_RS16205"
                     /old_locus_tag="AL025_15435"
                     /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_002305249.1"
                     /translation="MATIKVSRTTSCSRAINYAEPRATIKTGINCDVDYAKSEMKQIRM
                     LYGKDDRVQAHLLIQSFRPGEITAEKANQLGAEYAKKIAPDHQIAIYTHTDKDHIHNHI
                     VINSVNLETGKKFQAHGQAFLNKCYDLNDEICLAHNLPITERGKKPEKRTMSEIKLKEK
                     NEPVWKDEIRIAIDQTMKNKKTRTYDQFCNSLKTLGIHCFNRGKNFTYELIHKKKKVRS
                     NRLGKDYEKETILHELDRRERTYNQQRTNELRRARASIRETAEEVRREQRTLTPEQPEI
                     RPARRNHEQHVERGTDHQQELSL"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(1304..1684)
                     /gene="mobC"
                     /locus_tag="AL025_RS16210"
                     /old_locus_tag="AL025_15440"
     CDS             complement(1304..1684)
                     /gene="mobC"
                     /locus_tag="AL025_RS16210"
                     /old_locus_tag="AL025_15440"
                     /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="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_002317440.1"
                     /translation="MSEQNQNLASNSSKKYTYRSEPKQISFRVSESEFAKLKQSAEALQ
                     MSVPAFVKAKAQNARLVTPKVAPDIAQAIARDLAKAGGNINQIAKWCNTHQHDVASGDA
                     QRLSENLKIMQKELQKIWQQLR"
                     /name="mobC"
     gene            complement(2126..2263)
                     /locus_tag="AL025_RS16795"
     CDS             complement(2126..2263)
                     /locus_tag="AL025_RS16795"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002303562.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002303562.1"
                     /translation="MILLKKEYEKFYDRLIYSLQLPKKLNRQLQKTYETKSTEEWESYC
                     "
                     /name="hypothetical protein"
     gene            complement(2377..2997)
                     /locus_tag="AL025_RS16215"
                     /old_locus_tag="AL025_15445"
     CDS             complement(2377..2997)
                     /locus_tag="AL025_RS16215"
                     /old_locus_tag="AL025_15445"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002303561.1"
                     /GO_function="GO:0140359 - ABC-type transporter activity
                     [Evidence IEA]; GO:0005524 - ATP binding [Evidence IEA];
                     GO:0016887 - ATP hydrolysis activity [Evidence IEA];
                     GO:0042626 - ATPase-coupled transmembrane transporter
                     activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ABC transporter ATP-binding protein"
                     /protein_id="WP_002303561.1"
                     /translation="MILSVENFTLSINKKKIKQNWNFSISEKDFIIVTGKSGSGKTTLL
                     NNLSLIDKQYTGNLFYFEKKVSKHDIQRLRRNHISYLFQNYALLENQTVQYNFELAKKF
                     NSNISNDHIYNLLTDFSLPKDILKEKIFLLSGGEQQRIALIRNMLKPFDILFADEPTGN
                     LDKENSTFIMNFLKNLTEKEKKAVVLVTHDLNVLNYGTNIIEL"
                     /name="ABC transporter ATP-binding protein"
     gene            complement(2994..4034)
                     /locus_tag="AL025_RS17040"
     CDS             complement(2994..4034)
                     /locus_tag="AL025_RS17040"
                     /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_080341602.1"
                     /translation="MKKASKFVYKIQKNYKTFIIAPYNYATIQENNKEFFIGQKVYPNF
                     EDYVSQPAGAGICVDLNYLKYYNPISFEESTDLNLINSDPLTTYILVPKKYKEYAKMIE
                     KNYLEDIQFRLEDSPPQAPYKNPNLKNLKIKLIFVNNNQKYFSFNTLYGKAKDNYTITD
                     PIVRVINPEITESLFWGNILTSDGGLFFDQKHTSNQNFFNQINPYIKEFNLENIINFSY
                     SVFQETGELLSQKKVNKLNAYLQYLLILGLFIIINFQMIFVSFTINSKKIALKKIFGYS
                     PISQVLDLCLLPFTIELFATMCFQLIFSKNTYLYFIIFMIFLINLITSIIIYKKNSFKY
                     FKENIL"
                     /name="hypothetical protein"
     Typing          complement(412..1322)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.671"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttgaaacgat tatcaaggaa aatatacagc caagaaaaga aaaatcgctt aaatcgaatt
       61 ttagagcctt ttaatgaata tcttgtttga aaaattttat agatgagcca aatacttcct
      121 gaaatactaa caaaaatgag tagatagggt aaaataaaat gccattttag cctccccata
      181 ctaaccaaaa tgcgaacagt gtcaggacta agcaacataa gggggcaaga aaatccaatg
      241 atcgttgaat aagcaccttt tttctgttcc ttatttcgct ggtctaatag ctcttgatgg
      301 agttttttta acttgtaaat caatcgtagt ttgtatcctt tcttgcgtat aaggaacgag
      361 aaaagcacgt tgtttcttta tttcgttttc tatgtctttt taacgtttta gagcgataat
      421 tcttgttggt ggtctgttcc tctttcaacg tgttgttcat ggtttcttcg agccggtcta
      481 atttccggtt gttcaggcgt aagagttcgt tgttctcttc gtacttcttc tgcagtttcg
      541 cgaatgctag ctcgagctct tcgtagctcg ttggttcgct gttggttata ggttcgttct
      601 cgtctgtcca gctcatgtaa aatcgtctcc ttttcgtagt cctttcctag tctgttggat
      661 cgtacttttt tctttttgtg gatcaattcg taagtgaaat ttttcccgcg attgaagcaa
      721 tgaatcccca atgttttgag ggaattacaa aattggtcat aggttctggt ttttttgttt
      781 ttcattgttt gatcgatcgc aatccgaatt tcgtctttcc aaacaggttc atttttttct
      841 tttaatttta tttcagacat ggttcgtttt tctggtttct ttcctcgctc agtgattggt
      901 aagttatgtg caagacaaat ctcgtcattt aggtcataac atttgtttag aaatgcttga
      961 ccatgagctt gaaatttttt tccagtctcc agattaacgg agttaatgac aatgtgatta
     1021 tgaatatggt ctttgtctgt atgtgtgtaa atagctattt ggtgatcggg ggctattttt
     1081 tttgcatact ctgcccctag ttgattagct ttttcagcgg taatttctcc tggtcgaaaa
     1141 gattgaatca ataagtgtgc ctgtacacgg tcgtcttttc catacagcat gcgaatttgt
     1201 ttcatttcac ttttggcata atcgacgtca cagtttattc ctgttttaat ggttgctcgt
     1261 ggttctgcgt aattaattgc acgactacaa gaagtggttc ggcttacctt aattgttgcc
     1321 atatcttttg tagctccttt tgcatgattt ttaggttttc ggataaacgt tgagcgtcac
     1381 cagaagcaac gtcatgttgg tgtgtattgc accacttagc aatttgattg atattccctc
     1441 cagctttggc taaatcgcgc gcgattgcct gggcaatgtc tggcgccact ttcggtgtca
     1501 ccagacgcgc gttttgtgcc ttggctttca cgaaagccgg cacactcatt tgcaaagctt
     1561 cagccgattg cttcagcttt gcaaattcgg attcgctcac tcgaaaactg atttgttttg
     1621 gctcggatcg ataggtatat tttttagaag aattgctagc caaattttga ttttgttcgc
     1681 tcataagtcc caccctttca gtacgtccta cggacgtatc gttcgcaata ccattgtacc
     1741 taaaaaggta caatgagtaa agctcactaa aagggtttgg caagctctat atttgctagc
     1801 caaataccta cgtatttagt gcaaataacc gcttgtcaaa ggggcgcaag ctcccccttg
     1861 aatccccctc aaaagccacg ctccacaata caaaaaaagc tagcaaatgc tagccacttt
     1921 ttgtaaagtt tcgcttattt caccgaagat gaaattgttg ctttgcaaca aaaaacataa
     1981 atgctttttt gtgtaaacta ctaactattt agctaaaact gatagtttta ttaaacattc
     2041 agcaatattt ttagccaatt ttttatcaga ctttcggcga gtcattatga taatatgtcc
     2101 actttttgtt acttctacca aaaatctagc aataactctc ccattcttca gttgatttag
     2161 tttcataagt cttttgtaat tgacggttta atttttttgg caattgcaaa gaataaataa
     2221 gtctatcata aaatttttca tactcttttt tcaataaaat cacttgggtg cctccttttt
     2281 attaagtgat tatttaaatt ttgggatagg agagatggaa tataaaataa atacccgtgg
     2341 tgctagtttt aaatcagcta gcatcacggg taaaaattat aattctataa tattagttcc
     2401 atagtttaga acatttaagt catgtgttac tagtacaacg gctttttttt ctttttctgt
     2461 taaatttttc agaaagttca ttataaaagt tgagttttct ttatctaaat ttcctgtagg
     2521 ttcatctgca aataatatat caaatggttt taacatattt ctaattaatg ctattctttg
     2581 ttgttctcca ccgcttaaga gaaagatttt ttcttttaag atatcttttg gcaaagaaaa
     2641 atctgttaat aaattataaa tatgatcatt ggaaatatta ctgttaaact tttttgctaa
     2701 ttcgaaattg tattgtactg tttgattttc aagaagagca tagttttgaa ataaatagct
     2761 aatatgattt cttcgtagac gttgtatatc atgtttagaa actttctttt caaaatagaa
     2821 taagttaccg gtatattgtt tatctattag gcttaaatta tttaacagag tagtttttcc
     2881 actaccactt tttcctgtta ctataataaa atctttttct gatattgaaa agttccaatt
     2941 ttgtttgatc ttttttttat taattgacag ggtgaaattc tcaactgata atatcataaa
     3001 atattctcct taaaatattt aaaactattt tttttataaa taataataga agtaattaga
     3061 tttattaaaa agatcataaa aattataaaa tacaagtaag tgttttttga aaatatcaat
     3121 tgaaaacaca tagtagcaaa taactctatt gtaaaaggga gtaaacataa atctaaaact
     3181 tgacttattg gtgaatatcc aaatattttt tttaaagcta ttttttttga atttatagta
     3241 aaactaacaa aaatcatttg aaaattaatt attataaata atcctaatat taaaagatat
     3301 tgtagatatg catttaattt atttactttt ttttgagata ataattcacc agtttcttga
     3361 aaaacagaat aagaaaaatt tatgatattt tctaggttaa attcttttat atacggatta
     3421 atttgattaa aaaagttttg gtttgaagta tgtttctgat caaaaaataa tccaccatca
     3481 ctagtcaata tatttcccca aaataatgat tctgttattt ctggattaat aactctaact
     3541 atgggatcag ttattgtata gttatctttt gcctttccat ataaggtatt aaaactaaaa
     3601 tacttttggt tattattaac aaatattagt tttattttta aatttttcaa attaggattt
     3661 ttataaggag cttgaggagg agagtcctca agtctaaact gtatgtcttc taaataattt
     3721 ttttcaatca tttttgcata ttctttatat tttttaggta ctagaatgta agtagttagt
     3781 ggatcagagt ttattaaatt taagtcagta gattcttcaa aagaaatagg attgtaatat
     3841 tttagatagt ttaaatcaac acatattcct gcaccagcag gttgactaac atagtcttca
     3901 aaatttggat aaactttttg tccaataaaa aattctttat tattctcttg gatagttgcg
     3961 taattgtatg gcgcgataat aaaagtttta taattcttct gtattttata aacaaattta
     4021 ctagcttttt tcaagtagtt attttcttct acggtgttgt ttctatttaa ttgattagta
     4081 atatttgttt tgtataaatt agtagttctt tcccaatatt taagagaatt attttcggct
     4141 tcattatggg tatttattac ttttgtagaa gctattaaca gaaggatcat gcttaagaat
     4201 agacagatat ttaatataca aagatttaac ttaagtggtc gtgaattttt tagataattt
     4261 tttatactag ataaatgata gatacttaga gtaactatga taaataaaaa ctaattataa
     4321 aatgaaaaat actacataga agaaatgata ggaaaaaatt ttcgttactg taatatatgc
     4381 tcaaaaaaat agataaaatg aaagttataa tcaaagaaca aaataagagg tttaactctt
     4441 taatagaatc ttttatagta tcaaaagagt tatagcctaa catttttttt agagtgattt
     4501 ctttcatttt tgaaaaagca aatataattg tagtaattac aataaatata ctaagatagc
     4561 agataacaag aacaatatta gtattaattt gaaaagtatc tgattgattg atattggaaa
     4621 tagtaggtgt tccatatttt ttcagtacag gaattaattt gtttgagttt ccttgtacat
     4681 ataatatttc acttaatcca atattttcca catgagaaaa aggataaata tttatattta
     4741 aaaaattatt tggaagtttt aattggtact tagaattttt gttattagta taatgg
//
