LOCUS       NZ_CP066642             6303 bp    DNA     circular CON 20-FEB-2024
DEFINITION  Enterococcus faecium strain Dallas 144_1 plasmid p144_1_6kb,
            complete sequence.
ACCESSION   NZ_CP066642
VERSION     NZ_CP066642.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17038103
            Assembly: GCF_016415405.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 6303)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Molecular characterization of VREfm isolates from Dallas, Texas
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 6303)
  AUTHORS   Islam,M.J. and Palmer,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-DEC-2020) Biological Sciences, University of Texas at
            Dallas, 1520 Richardson Dr Apt 1418, Richardson, TX 75080, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 2019
            Assembly Method                   :: Unicycler v. 0.4.7
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 266.0x
            Sequencing Technology :: Illumina NextSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/20/2024 02:43:36
            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)                     :: 3,211
            CDSs (total)                      :: 3,120
            Genes (coding)                    :: 3,025
            CDSs (with protein)               :: 3,025
            Genes (RNA)                       :: 91
            rRNAs                             :: 6, 5, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 5, 6 (5S, 16S, 23S)
            tRNAs                             :: 70
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 95
            CDSs (without protein)            :: 95
            Pseudo Genes (ambiguous residues) :: 0 of 95
            Pseudo Genes (frameshifted)       :: 33 of 95
            Pseudo Genes (incomplete)         :: 51 of 95
            Pseudo Genes (internal stop)      :: 27 of 95
            Pseudo Genes (multiple problems)  :: 13 of 95
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066642.1.
            Bacteria and source DNA available from Dr. Kelli Palmer, UTDallas.
            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..6303
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="Dallas 144_1"
                     /isolation_source="rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="p144_1_6kb"
                     /geo_loc_name="USA: Dallas"
                     /collection_date="2015"
     gene            join(6063..6303,1..674)
                     /locus_tag="JCP95_RS15850"
                     /old_locus_tag="JCP95_15850"
     CDS             join(6063..6303,1..674)
                     /locus_tag="JCP95_RS15850"
                     /old_locus_tag="JCP95_15850"
                     /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_002321380.1"
                     /translation="MATVKVSRTTSCSRAINYAEPRATVKTGINCDIDYAKSEMKQIRT
                     LYGKDDRVQAHLLIQSFRPGEITAEKANQLGAEYAKKIAPNHQIAIYTHTDKDHIHNHI
                     VINSVNLETGKKFQAHGQAFLNKCYDLNDEICLEHDLTITERGKKTEKRTMSEIKLKEK
                     NEPVWKDEIRFAIDQTMKNKKTRTYTQFCDSLKTFGIHCLNRGKNFTYELVHKKKKVRS
                     NKLGKDYEKETILHELDRRERTYNQQRTNELRRARASIRETAEEVRREQRTFTPEQSEI
                     RPTRRNHEQHVERGTDHQQELSL"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            919..1608
                     /locus_tag="JCP95_RS15855"
                     /old_locus_tag="JCP95_15855"
     CDS             919..1608
                     /locus_tag="JCP95_RS15855"
                     /old_locus_tag="JCP95_15855"
                     /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_002321377.1"
                     /translation="MAFYLPYLLISASILGIIWLSYKAYQTRYSLKGSKIRFKRFLLVG
                     VIFALSIVLSGLFGVLEGNKRVSRSILLGDITQKYEAACDKKKKEQALAQKMEEFTACY
                     EDMNNIFVDQEKRLTDKNMKKLTRFYQNLPEKQQKEVQEKYEQVKKDVQYFKDTQTEEA
                     CCNLFSDTIPFSTSEQERKERQQSVTYERYETLLQQATNIQNPTKKETALNYLESVKEW
                     LDQQQQN"
                     /name="hypothetical protein"
     gene            2491..3441
                     /locus_tag="JCP95_RS15865"
                     /old_locus_tag="JCP95_15865"
     CDS             2491..3441
                     /locus_tag="JCP95_RS15865"
                     /old_locus_tag="JCP95_15865"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002303559.1"
                     /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_033642128.1"
                     /translation="MANEIVKYHHELNTIPLRKFTPVEMNLFFSIVSRMREKGDKTVRL
                     TFDQLKDLSNYKATANNRFINDLEMTYDKLMDLRFGKRSANGLDIDRFVMFSEFKIRGT
                     AKDPYVDIQVYEKALPLLNNLDEWVRYSLQQFNELQSSYAKTMFRLLKQYRTKGFAYFS
                     KEDFHELLDIPKSYWNNQANVDNRVIKPIRQELTAIFKGLSIKKKYGKGRGKPVVGYQF
                     TFKPEIKKADDFNKHAPTKEEQNKALALADKQKEYEEPATTINEKIKQKKRELELLQQI
                     KQLEKEKEALEKQTESALSKKEKKSLLSDLDNLFQ"
                     /name="replication initiation protein"
     gene            3462..3995
                     /locus_tag="JCP95_RS15870"
                     /old_locus_tag="JCP95_15870"
     CDS             3462..3995
                     /locus_tag="JCP95_RS15870"
                     /old_locus_tag="JCP95_15870"
                     /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_002321384.1"
                     /translation="MQPQETFTIKELSELFKMSRQAISKHIQKLDSSMIAKNERGYKVV
                     LRSGVLQLARNLGNQMLLDRLHEYEQDNDKNVNIPSKNVVTNKLLDQLREENEFLREQL
                     ALREQNNSHIQKLLDQQQQLTLQANKQIEKLQEKLQLTYTEEAPENDSTTLSEATETID
                     KQIDTEKKWWQLWK"
                     /name="DUF536 domain-containing protein"
     gene            4011..4181
                     /locus_tag="JCP95_RS15875"
                     /old_locus_tag="JCP95_15875"
     CDS             4011..4181
                     /locus_tag="JCP95_RS15875"
                     /old_locus_tag="JCP95_15875"
                     /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_002292472.1"
                     /translation="MTRKNLLFGSILLGILGFSPMLLSVINKGNKHGELKLNPNYYNSP
                     NEELFVKETDK"
                     /name="hypothetical protein"
     gene            4631..5164
                     /locus_tag="JCP95_RS15880"
                     /old_locus_tag="JCP95_15880"
     CDS             4631..5164
                     /locus_tag="JCP95_RS15880"
                     /old_locus_tag="JCP95_15880"
                     /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"
     gene            5176..5379
                     /locus_tag="JCP95_RS15885"
                     /old_locus_tag="JCP95_15885"
     CDS             5176..5379
                     /locus_tag="JCP95_RS15885"
                     /old_locus_tag="JCP95_15885"
                     /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            5701..6081
                     /locus_tag="JCP95_RS15890"
                     /old_locus_tag="JCP95_15890"
     CDS             5701..6081
                     /locus_tag="JCP95_RS15890"
                     /old_locus_tag="JCP95_15890"
                     /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_002321381.1"
                     /translation="MSEQHQNLASDHSKKYTYRSEPKQISFRVSESEFAKLKQSAEALQ
                     MSVPAFVKAKAQNARLVTPKVAPDIAQAIARDLAKAGGNINQIAKWCNTHQHDVAPDDA
                     QRLSENLKIMQKELQKIWQQLK"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          2493..3441
                     /name="rep_cluster_1197"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.953"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          4..671
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.274"
                     /coverage="99.0"
                     /evalue="1.77e-137"
     Typing          6064..6302
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.75"
                     /coverage="99.0"
                     /evalue="7.36e-44"
ORIGIN
        1 aaaaaatagc ccctaaccac caaatcgcga tttacacaca tacagacaaa gaccatattc
       61 ataatcacat tgtcattaac tccgttaatc ttgaaactgg gaaaaaattt caagcccatg
      121 ggcaagcatt tttaaacaaa tgttatgacc taaatgacga gatttgtctt gaacatgact
      181 taacaatcac ggaacgagga aagaaaaccg aaaaacgaac catgtctgaa attaaattaa
      241 aagaaaaaaa tgaaccggtt tggaaagacg aaattcggtt tgcgattgat caaacaatga
      301 aaaacaaaaa aactcgaacg tatacccaat tttgtgattc acttaaaaca ttcggcattc
      361 attgcttgaa tcgcggaaaa aattttactt acgaattggt ccacaaaaag aaaaaagtac
      421 gatccaacaa actaggaaag gattacgaaa aggagacgat tttacatgag ctggacagac
      481 gagaacgaac ctacaatcaa caacgaacca acgagctacg aagagctcga gctagcattc
      541 gcgaaactgc agaagaagta cgaagagaac aacgaacttt tacgcctgaa caatcggaaa
      601 ttagaccgac tcgaagaaac catgaacaac acgttgaacg aggaacagac caccaacaag
      661 aattatcgct ctaaaacgtt aaaagacatc gaaaacgaaa taaagagaca acgtgccttt
      721 cttgcgcctt atacccaaga aaggatacaa actacgatgg attcacaagt caaaaaactc
      781 caccaagcgc tattagacca gcgaaaccaa gaacaaaaaa aggctttaat tcaacgatcg
      841 atggatattc ttgccccctt atgttgctta gtactaacat tattagcctt ttggttggta
      901 tggggagaat aaacagacat ggcattctat ttaccctatc tactcatttc tgccagtatt
      961 ttaggaatta tttggcttag ctataaggct tatcaaacaa gatattcatt aaaaggctct
     1021 aaaattcgat ttaagcgatt tttattggtc ggggttatat ttgccttatc aatcgtttta
     1081 agtggtttat tcggcgtttt agagggtaat aaacgtgttt caagaagcat tttattaggg
     1141 gatatcactc aaaagtatga agcagcatgt gataaaaaga aaaaagagca agcattagca
     1201 caaaaaatgg aggaatttac cgcttgttat gaggacatga acaatatttt tgtggatcaa
     1261 gagaaacgtt taacagataa aaacatgaaa aaactcactc gtttttatca aaacttacca
     1321 gaaaaacagc aaaaagaggt acaagaaaaa tatgagcaag taaaaaaaga cgtgcaatat
     1381 tttaaagata cgcagacaga agaagcttgt tgtaacttat ttagcgatac aatccctttt
     1441 tcaaccagtg aacaagaacg aaaagaacgg caacaatcgg tcacatacga acgttatgaa
     1501 acactgcttc agcaagcaac aaacatacaa aatccaacga aaaaagaaac ggcattaaat
     1561 tatctagaaa gtgtcaagga atggttggat cagcaacaac aaaattgaat ttgattagca
     1621 atcatgttaa actgaacctg caaatgatca aacattagat acacgaaagc cccagagagg
     1681 tcggattctc tggggctttt tttcaggttg atgtcgcctt tattgatttt acttcttgtt
     1741 tcggttattc aaccaataac tgaataaaga gacacaaact tctacaagaa gggggcaaat
     1801 gaaccgttca aacattagat acacctcctt ccagtcgcaa gactgtcgga taggcgacaa
     1861 gttattatac cttacaaaat aaaatctgtg tggtgttttt aagtatccct tattttcggg
     1921 ttgttagggc ttgccctgac cgcctgtaag gcgctttaag aacaagataa ggttttttac
     1981 ccaagactgt cttaaaacga cttagacgag ctatcagagg cttcccccac ctccgttact
     2041 gacttgtttt tagcaaagga gcctttaggc gactgcgcag tacaatgtga gagcatagcg
     2101 atcacacttt tttagcgacc gtagggagca aggttttgaa ttggcagttt tgaaaaatgc
     2161 gcgaacctgt tggtagaaaa aagaagtggt ttttaggcgg gaaattttgt caccctcttt
     2221 tataatctct ttttaaacct ttttttaaac ctctttaccg tcggctgtgt ccttactcct
     2281 tcaatggata cagcgtttta taaactacat tttgtctgct tttaaactac attttgtctg
     2341 cttttaaact acattttgtc tgcttttaaa ctacattttg tctgctttta aactcttttt
     2401 ttgcactcac gtatgttata atatgcatta tcacagacaa aacgttgttt ataacgtctg
     2461 tatccattga aggagtaagg aggaatatct ttggcaaatg aaatcgtgaa ataccatcat
     2521 gaattaaata ccattccgtt gcggaaattt acaccagttg aaatgaatct atttttctct
     2581 attgtgtcta gaatgcgcga aaaaggcgat aaaacagtcc gtcttacttt tgaccaacta
     2641 aaagatttaa gtaattataa agcaactgct aataatcgtt tcattaatga tttagaaatg
     2701 acttatgata aattaatgga tttacgtttt ggtaaaagaa gtgctaatgg gctcgatata
     2761 gatagattcg ttatgtttag tgagtttaaa atacgtggaa ctgctaaaga tccatatgta
     2821 gacatacaag tttacgaaaa agctttacct ttactaaaca atttagatga gtgggttcgc
     2881 tattcactcc aacaatttaa cgaattacaa agtagctatg caaagactat gtttcgatta
     2941 ctaaaacaat atcgaactaa aggttttgct tatttttcta aagaggattt tcatgaacta
     3001 ttagatattc caaaaagtta ctggaacaac caagcaaacg ttgataatcg tgttataaag
     3061 cctatacgac aggaattaac cgcaatcttc aaaggattat caatcaaaaa gaaatacgga
     3121 aaagggcgag gaaaacctgt cgttggctat caatttacgt ttaaaccaga aatcaaaaaa
     3181 gcagatgatt ttaataaaca tgcaccaacc aaagaagaac aaaataaagc attggcttta
     3241 gctgataaac aaaaagaata cgaagaacct gctacaacaa ttaacgaaaa aatcaaacag
     3301 aagaaacgag aacttgaact cctccaacaa atcaaacaac tagaaaaaga gaaagaagct
     3361 cttgaaaaac aaacagagtc cgcactttcg aaaaaagaga aaaaaagttt attatctgat
     3421 ttagataatt tattccagta gcaacctagg aggcaaccag tatgcaacca caagaaacct
     3481 ttacaataaa ggaattgtca gaacttttta agatgagtag gcaagcaata tcgaaacata
     3541 tccaaaaatt agattcttcc atgatagcta aaaatgagcg tggttataag gttgtattgc
     3601 gttctggagt attgcaactt gctcgcaact taggcaacca aatgttgcta gataggttgc
     3661 acgagtacga acaagacaac gataaaaatg ttaatatacc aagcaaaaac gtggttacaa
     3721 acaagttgct agatcagttg cgtgaagaaa atgaattttt acgagaacaa cttgccctca
     3781 gagagcaaaa taattctcat atacaaaaac tactcgacca gcaacaacaa ctcaccctac
     3841 aagccaacaa acaaatcgaa aaactgcaag aaaaactaca gttgacttat acagaagaag
     3901 ctccagagaa tgactcaacg actctttctg aagcaacaga aacaatagac aaacaaattg
     3961 atactgaaaa aaaatggtgg caactttgga aataactgga gggaacattc atgacaagaa
     4021 aaaatcttct attcggttct attttactag gaattctagg attcagtccg atgttattgt
     4081 cagtgatcaa taaagggaat aaacatggtg aattgaaatt gaatccaaat tattacaaca
     4141 gtcctaacga agaattgttt gtaaaagaaa cagataaata ataaaaaaga ctgctctttc
     4201 gagcagccag ttaaaaaata atgagtgttt attcttgaaa aagcaacgcg cttatgaagc
     4261 gctaccaaaa atttatcata ttttattaaa aataacaacc cagtaaaaaa tgactggtaa
     4321 aaattcacaa agaaacggaa agaagcaacc gcagaaaatc aagcttaaaa agagcttttg
     4381 acctagacca atcgaaaatc acaaagtgag cctctgtatc ggttgataca agggctactt
     4441 ggcatagtac acattatgtc aacaagaatt taatataaca tattttccta atgcattcta
     4501 actataccac attatcaaaa atataaatta tctttactaa ataaaatatt gacaagccta
     4561 taccttttgt tttatgattt tcacaaagaa aacgttttct atatattttt ctgtatcagg
     4621 aggaaattct atgaaaaaat ttactttagg ggtagctttg ttaactattg gggcagttgt
     4681 tttaccgtca actactatag tttatgcttc agaaaattcc caagtggtat cattaaacga
     4741 aaacaatgct actgaaaatg tagttattga gtacactgaa gatggtatgg tcgtaactaa
     4801 atatgaggat ggttatagtg cggaagattt tgcaaattct tcagatatca tgacaagagc
     4861 tgcagttgca agatggggca aaaaggaata tacaaatatt gctgtaacca ctggagtagc
     4921 tgctaatgct attaatgctg ccttttgggc aggagggaaa gctagcactt ctatgtttgg
     4981 tatcccaggt tgggcaattg gtgctttgtt aacaggtgca agttggacta aaaaaggtgc
     5041 ttctccaggg aatgcagttg caaaagaatg ggacaaaaat ggtaatggct ggattggatt
     5101 ttattaccaa aggggatatg atgcagctgg aagagttgta gctactagat attcaacgtt
     5161 ataagttaag gagtgatgtt tttgatatct aaatcattaa aatcattaaa aacatttact
     5221 aaaaagaatc cgcaaatagc tactattcgt atttttatat ttgctatagc tgttgctata
     5281 attgttaata tgctaagcgg agggcaatta tacaaatctg gtttattttt agtgttaatc
     5341 ttagttgtct tagacataat aaagtctaaa aaaaaataaa tcgatacatt ttagaagaat
     5401 agggttgttt gaatattaca aagcaacaat ttcaccttcg gtgaaataag cgaaacttta
     5461 caaaaagtgg ctagcaaatg ctagcctttt tttgtattgt ggagcgtgga ttttgagggg
     5521 gattcaaggg ggagcttgcg ctcctttgac aagcggttat ttgcaccaaa tacggaggta
     5581 tttggctagc aaatatagag cttgccaaac ccttttagtg agctttactc attgtacctt
     5641 tttaggtaca atggtattgc gaacgatacg tccgtaggac gtactgaaag ggtgggactt
     5701 atgagcgaac aacatcaaaa tttggctagc gatcattcta aaaaatatac ctatcgatcc
     5761 gagccaaaac aaatcagttt tcgagtgagc gaatccgaat ttgcaaagct gaagcagtca
     5821 gctgaagctt tgcaaatgag tgtgccggct ttcgtgaaag ccaaggcaca aaacgcgcgt
     5881 ctggtgacac cgaaagtggc gccagacatt gcccaggcaa tcgcgcgcga tttagccaaa
     5941 gctggaggga atatcaatca aattgccaag tggtgcaata cacaccaaca cgacgttgct
     6001 cctgatgatg ctcaacgttt atccgaaaac ctaaaaatca tgcaaaagga gctacaaaag
     6061 atatggcaac agttaaagta agtcgaacca cttcatgtag ccgagcaatc aattacgcag
     6121 aaccacgagc aaccgtcaaa acaggaataa actgtgacat tgattatgcc aaaagtgaaa
     6181 tgaaacaaat acgcacgctt tatggaaaag acgatcgtgt acaagcacac ttattgattc
     6241 agtcctttcg accaggagaa attaccgctg aaaaagccaa tcaactaggg gcagagtatg
     6301 cga
//
