LOCUS       NZ_CP094233             5275 bp    DNA     circular CON 11-APR-2024
DEFINITION  Enterococcus faecium strain NY13320 plasmid pNY13320-3, complete
            sequence.
ACCESSION   NZ_CP094233
VERSION     NZ_CP094233.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN26755017
            Assembly: GCF_022749455.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 5275)
  AUTHORS   Zhou,D.
  TITLE     Complete sequence of strain NY13320
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5275)
  AUTHORS   Zhou,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-MAR-2022) State Key Laboratory of Pathogen and
            Biosecurity, Beijing Institute of Microbiology and Epidemiology, No.
            20, Dongdajie, Fengtai, Beijing, Beijing 100071, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP v. v 3.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology             :: PacBio RSII
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022749455.1-RS_2024_04_11
            Annotation Date                   :: 04/11/2024 17:08:02
            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)                     :: 3,121
            CDSs (total)                      :: 3,029
            Genes (coding)                    :: 2,884
            CDSs (with protein)               :: 2,884
            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)              :: 145
            CDSs (without protein)            :: 145
            Pseudo Genes (ambiguous residues) :: 0 of 145
            Pseudo Genes (frameshifted)       :: 70 of 145
            Pseudo Genes (incomplete)         :: 66 of 145
            Pseudo Genes (internal stop)      :: 35 of 145
            Pseudo Genes (multiple problems)  :: 20 of 145
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP094233.1.
            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..5275
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="NY13320"
                     /host="Homo sapiens"
                     /db_xref="taxon:1352"
                     /plasmid="pNY13320-3"
     gene            485..1234
                     /locus_tag="MPN36_RS15175"
                     /old_locus_tag="MPN36_15175"
     CDS             485..1234
                     /locus_tag="MPN36_RS15175"
                     /old_locus_tag="MPN36_15175"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002322914.1"
                     /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_002322914.1"
                     /translation="MGQPNKKADIALKDLLSRQDYLVVQGNDLAKAFGGLKSFEQRVLD
                     YCFSFVTKDSKLDDEYEVTALEIIKHFGLNTSGDSYRRIAEAFKKLNENTALYLRVERP
                     DGTQGLRMTQLFSWIDFYADGLVRFKFSADSAPYVLDLKEKFYSFRLGELSRINGKYAL
                     IMLKLWESYRRGKEKHTTITGDLEEWESWFLGKDKRLPAGQFFQKVITRAIEELSDKMS
                     VSFFVTTLKRGRKVVGYEITINDTSKE"
                     /name="replication initiation protein"
     gene            1248..1397
                     /locus_tag="MPN36_RS15180"
                     /old_locus_tag="MPN36_15180"
     CDS             1248..1397
                     /locus_tag="MPN36_RS15180"
                     /old_locus_tag="MPN36_15180"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002322915.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002322915.1"
                     /translation="MKKRLRKKMAKKNSSLDQAMKELMNYAKGERDGFLIHSYDEKGEQ
                     KNDG"
                     /name="hypothetical protein"
     gene            1387..1548
                     /locus_tag="MPN36_RS15185"
                     /old_locus_tag="MPN36_15185"
     CDS             1387..1548
                     /locus_tag="MPN36_RS15185"
                     /old_locus_tag="MPN36_15185"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002322916.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002322916.1"
                     /translation="MTAKTVTIDVEQLEKLLERHSDAIIEYTGGLSEETINQFDLLLTE
                     IIELDSKE"
                     /name="hypothetical protein"
     gene            1557..1922
                     /locus_tag="MPN36_RS15190"
                     /old_locus_tag="MPN36_15190"
     CDS             1557..1922
                     /locus_tag="MPN36_RS15190"
                     /old_locus_tag="MPN36_15190"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002322917.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002322917.1"
                     /translation="MAKMDIEDLEKKLAEARHDLSVKIGTNMVEKQGFKSYSAYNTFMR
                     NASKALKSSAGSAPAPAAAKPVATSAEKLPSELKAEAVQFQKQLEKWMEDNWGNKLDYK
                     TFYPELLEFFQKLNSLE"
                     /name="hypothetical protein"
     gene            2478..2834
                     /locus_tag="MPN36_RS15195"
                     /old_locus_tag="MPN36_15195"
     CDS             2478..2834
                     /locus_tag="MPN36_RS15195"
                     /old_locus_tag="MPN36_15195"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002323247.1"
                     /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_029404142.1"
                     /translation="MSEQKLNAENRKDSRQIKFRVSEDEYQYLTAIADQTGMSVPQLCK
                     SVALGMKYRAPNVDREGAIQIAKELRKYGGNLNQMARFINMNKGQMPSSSDLALMNQQL
                     SQIEKGVIDLWEQL"
                     /name="plasmid mobilization relaxosome protein MobC"
     gene            2819..3805
                     /locus_tag="MPN36_RS15200"
                     /old_locus_tag="MPN36_15200"
     CDS             2819..3805
                     /locus_tag="MPN36_RS15200"
                     /old_locus_tag="MPN36_15200"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002351099.1"
                     /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_002322919.1"
                     /translation="MGATLALKGGKRGASALIGYVNRHGKLDRDRIYTHKLSAENKLAQ
                     TQLEATRRIFAKTGGIQAFHWVQSFDNSFDKNNPADVQKAHEIGAKLVDEIAKSYPNHE
                     IYMGTHTDSESGYIHNHIVFASIDTETGKKFHSDTEVGYHLQDLNDKVLLSFGIEQPKE
                     KFKQVDFEMHAEGKMSNREKMKHMILGAQDMSTDFDSFKKNLQEAYAVEVYEYNKGKRI
                     GFKWVDDEGKDFTIGGRKLGSDFERPAIERTLEFSQQKQEKEVEKPLETKPKVTNDDFS
                     ISGLKNLANDIRQQEERKKKEELQRQKEIERQQRSRPFYHDRGGMER"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            3813..4268
                     /locus_tag="MPN36_RS15205"
                     /old_locus_tag="MPN36_15205"
     CDS             3813..4268
                     /locus_tag="MPN36_RS15205"
                     /old_locus_tag="MPN36_15205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002322920.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002322920.1"
                     /translation="MPLDDFASKQELQKVKQELAEIKQQNQEVIETLKSLDNSVKQGYI
                     KVRGGEDIPKMSELKAEMNRYATYVQKRTAEIDQKLDSYGNISKSVSDELSRQVRPQVQ
                     KFLANDDRATAEELKQNRIANLMSVLASVGLFIGGTAILIVSVLKLL"
                     /name="hypothetical protein"
     gene            4296..4793
                     /locus_tag="MPN36_RS15210"
                     /old_locus_tag="MPN36_15210"
     CDS             4296..4793
                     /locus_tag="MPN36_RS15210"
                     /old_locus_tag="MPN36_15210"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002322921.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002322921.1"
                     /translation="MKLFFEKMGWHILPVVIILVGSYSLFCIFRSILEKFEEPKLKRVV
                     FALCFAFLALFVSVGISSYRPDVALSVRPKISKIEQLEAKAEAKQKKIDKISDQLEQAL
                     KIASQEKLKTFNPKDYPSEVITADWVQKNRDVIATLPDKELKDRYTKRFDDVESYFELN
                     SQ"
                     /name="hypothetical protein"
     gene            complement(4947..5045)
                     /locus_tag="MPN36_RS15215"
                     /old_locus_tag="MPN36_15215"
     CDS             complement(4947..5045)
                     /locus_tag="MPN36_RS15215"
                     /old_locus_tag="MPN36_15215"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019775148.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type I toxin-antitoxin system Fst family toxin"
                     /protein_id="WP_110958386.1"
                     /translation="MYEKFLTLVVAPLFVGLVIELVSHWLDEKDDN"
                     /name="type I toxin-antitoxin system Fst family toxin"
ORIGIN
        1 acaacggttt tgaccttaac gaaggagcgc aggcgactgc tgtaagcaaa atgtgagagc
       61 gtagcgatca ctcctttatg ccttgtggct gtaagattga acgaggtaaa ggggataaat
      121 tgtcgatgat gtgagaagca gtttatttca tgcgcgaacc tgttggaaaa aaatagacaa
      181 ctggtttggg cgggattttt ttttttttga atttaaattt ttttctcacc cgcgcgctta
      241 aagagaatac tttatagatt acttttaaat actttaaaat actttagggg aaaaggaatg
      301 gctttatacc agcgtttgta gcgcctataa atactatttt ccacgttgaa aatactattt
      361 tccacgtcaa aaatactatt ttccacgtca aaaatactat tttccacgtt gaaaattcaa
      421 atattgcaaa aaaactgaat aaatggtatt attttaaaaa aagtacaaaa ggaggatttt
      481 cagtttggga caaccaaata aaaaagctga tattgcatta aaagacttac taagccgtca
      541 agattattta gtagtgcaag gaaacgactt agctaaggca tttggagggc ttaaatcgtt
      601 tgagcaacga gttttagact actgttttag ctttgtaact aaagattcaa aactagatga
      661 cgaatacgag gtaaccgcat tagaaattat caaacatttt gggttgaaca cctctggaga
      721 ttcttaccgt cgaatagctg aagctttcaa aaagcttaat gaaaatactg cgctttatct
      781 tcgtgtcgag cgccccgatg gtactcaagg tctcagaatg acgcaattat tttcttggat
      841 tgatttttat gctgacgggt tagtaagatt caaattttct gctgattcag ctccatacgt
      901 tcttgatctc aaagaaaagt tttatagctt tcgtttaggt gaattatctc ggatcaatgg
      961 gaaatatgct ctcataatgt taaaactctg ggaatcctac cgtagaggaa aagaaaaaca
     1021 cacaacgatt acaggtgatt tggaagaatg ggaatcttgg tttcttggta aagacaaacg
     1081 ccttcctgca ggtcaatttt ttcaaaaagt aattactcgt gctattgaag aattatctga
     1141 taagatgtca gtttcatttt tcgtcacaac cttaaagcgt gggcgaaaag tcgttggata
     1201 tgaaatcacg atcaatgaca ccagcaaaga atagaggagt gatttagttg aaaaaaagac
     1261 tgcgtaaaaa gatggcaaag aaaaattctt cgctagatca agctatgaaa gaactaatga
     1321 actatgcaaa aggcgaacgt gacggctttt tgattcatag ttatgacgaa aaaggagaac
     1381 aaaaaaatga cggctaagac agttacgatt gacgttgaac agcttgaaaa gctgttagaa
     1441 aggcatagtg acgctattat tgaatacacc ggtggacttt cagaagaaac gatcaaccaa
     1501 tttgatcttc ttctaacgga aattatcgaa ctagattcta aggagtgagt ttacgcatgg
     1561 caaaaatgga tatcgaagat ttggaaaaaa aattagctga agctcggcat gatctttcag
     1621 tcaaaatcgg tacaaatatg gttgaaaaac aagggttcaa gagctattcc gcctacaata
     1681 ctttcatgcg gaatgcgtca aaggcattga agtcgtccgc cggatctgca cctgcgccag
     1741 cagctgcaaa gccggtggcc acttctgccg aaaaattgcc tagcgagctg aaagccgaag
     1801 cggtgcaatt tcaaaagcaa ctcgaaaaat ggatggaaga caactgggga aacaagttgg
     1861 attacaaaac attttatcct gagttgctag agttcttcca aaaattgaac agcttggaat
     1921 agcggaacga gctagtccat gcgatcaatt tttgaagaac gagcaagccg atttttggct
     1981 tgcttttttg tttgcctgcg aacagcgggc aaacaaaaaa ataaggtcaa cttgcgtgca
     2041 agtttgaccg catgagccag tagaaaaata gtcgaacaga ctactttttc tgaggcgaaa
     2101 tcacgtaata aaaatagccg aacaggctac tttttgttgc gtgattgggg gagttcgtag
     2161 ggggcaacgc cacctcgaca agcgatgtat ttgggtacca aatgcggtgc ttgcgtatta
     2221 tatgatttat taaccttgtt atgcgaccga atagggagta tgatgaggtt aataaatcat
     2281 tcggttatag agcggaaaaa gggaagtgac cgagtaggga actttcattt tgtagtggca
     2341 taaccgaggg agatttcatt gcggaaaaaa ggcgactgaa tagggagcgt ttttgtagct
     2401 ttgaatatcg accacgaaga atgacgagaa gaaaaaagcg accgaatagg gagcattttt
     2461 atttgaggag tgatgagatg agcgagcaga aattgaatgc cgaaaatcga aaagatagtc
     2521 ggcaaattaa atttcgagtg agcgaagacg agtaccagta tttgaccgcc attgcggatc
     2581 aaactggtat gagtgtgcca cagctctgca agagcgtggc acttggcatg aagtatcgag
     2641 cgccgaacgt tgatcgggag ggggcgatac aaattgccaa agagttgcgc aaatatggcg
     2701 gaaatctcaa tcagatggct cgctttatta acatgaataa ggggcaaatg ccttcaagtt
     2761 cagatttagc cttgatgaac cagcaacttt cgcaaatcga aaagggggtg attgacttat
     2821 gggagcaact ttagctttaa aaggcggtaa acgtggggct tctgcgctga ttggctatgt
     2881 aaatcggcat ggaaagcttg atcgtgaccg catttatacg cacaaactgt cagctgagaa
     2941 taaattggct caaactcagc tagaagcgac tagacggatt ttcgccaaaa caggcggtat
     3001 tcaagccttt cattgggttc aatcgtttga taattcgttt gacaaaaaca atccggcgga
     3061 cgtgcaaaaa gcgcatgaga tcggtgctaa actcgttgat gaaatcgcaa aaagctatcc
     3121 caatcatgaa atctacatgg gcactcatac cgattcagaa tccggctata ttcataatca
     3181 cattgttttc gccagtatcg acactgaaac cggtaaaaaa tttcactctg ataccgaggt
     3241 cggctaccac ctacaagacc taaacgataa ggttttattg agttttggca ttgaacagcc
     3301 gaaagaaaaa ttcaaacaag ttgattttga aatgcacgcc gagggcaaaa tgagtaatcg
     3361 agaaaaaatg aagcatatga tcctgggcgc acaagatatg agtaccgatt ttgattcttt
     3421 caaaaaaaat cttcaagaag cctatgctgt cgaggtttat gagtacaata aaggcaaaag
     3481 gattggcttc aaatgggtcg atgatgaggg caaagatttc acaatcggcg gacgaaaatt
     3541 aggttctgat tttgagcgcc ctgcgatcga acgaacactt gaattttctc aacaaaaaca
     3601 agaaaaagaa gtcgaaaaac cgcttgaaac caagcctaaa gtcaccaatg atgacttttc
     3661 tatcagcggt ttgaaaaatc ttgctaatga tattcgtcag caagaagaac gcaagaaaaa
     3721 agaggagctg caacgacaaa aagaaatcga gcgtcaacaa cgttctcgcc cgttctatca
     3781 tgatcgtggt ggcatggaaa ggtagtgacg atatgccgtt agatgatttt gcaagtaagc
     3841 aggagcttca aaaagtgaag caggaactag cggaaatcaa gcaacaaaat caagaagtca
     3901 ttgaaacgct gaaaagcctt gataacagcg taaaacaagg ctatatcaag gtgcgaggtg
     3961 gcgaagatat tcccaaaatg agcgagctga aagctgaaat gaaccgctac gccacctacg
     4021 ttcaaaaaag aaccgctgaa atcgaccaaa agcttgatag ctacggtaat atcagcaaat
     4081 ctgtatctga cgaattgagc cggcaagtgc gcccacaagt ccaaaaattt ttagccaacg
     4141 atgatcgagc gactgccgaa gagctgaaac aaaatcgaat agcgaattta atgtccgtat
     4201 tagcctctgt ggggcttttt atcggtggca ctgctattct tattgtttca gtcctaaagc
     4261 tcctgtaatc gaacgagagg gggcttaaaa cgcaaatgaa actgttcttt gaaaaaatgg
     4321 ggtggcatat tcttcctgtc gtgattattt tggtcggttc gtatagttta ttctgcattt
     4381 ttcgctcgat cttagaaaaa tttgaggaac caaagctgaa acgtgtcgtt tttgccctct
     4441 gttttgcgtt tctagcgctt tttgtgtcgg tcggcatttc ttcataccgt ccggacgttg
     4501 cgctgtctgt acgccctaaa atcagcaaaa tagagcaact agaagcgaaa gccgaagcaa
     4561 aacagaaaaa aattgataaa atttcggacc aactggagca ggcattgaaa attgccagtc
     4621 aagaaaagct gaaaaccttt aacccaaaag actatccaag cgaagttatt acggcggatt
     4681 gggtacaaaa aaatcgtgac gtgatcgcta ctttgcccga taaagagctg aaagaccgct
     4741 acacaaagcg atttgacgat gtagaatcct attttgagct gaatagtcag tgaaattgag
     4801 atttgccaac gtccatgcta taataaccat gcgaaaacgt tagaattttt tcgagtgcgg
     4861 aatgcacaaa agccagacac catgcgacgg tgtctggctt ttttttcgcc ctgcgactag
     4921 gcgtgtgagt tggaaggcac taagccttag ttgtcgtctt tctcgtccaa ccaatgagaa
     4981 actagctcaa tgactagccc gacaaatagc ggtgcgacaa ccaacgttag aaatttttcg
     5041 tacatacgga atacacctcc caacctgtgt aagcgttagt tggctttagt gccaagatta
     5101 atatagcatt cactccctgc aaaaaaaaga tggtctacca gatggggctt ttgggtcgtt
     5161 agggcttgcc ctgaccgcct gtaaaggcgc tgtataacaa gactaacgat ttaatctaaa
     5221 tcagtctaaa aacttgctac aacaagcttt tacgcctatc ccaaccgctc cttga
//
