LOCUS       NZ_CP097065             5254 bp    DNA     circular CON 19-MAY-2024
DEFINITION  Enterococcus faecium strain AT02 plasmid pAT02-d, complete sequence.
ACCESSION   NZ_CP097065
VERSION     NZ_CP097065.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN28025445
            Assembly: GCF_023299805.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 5254)
  AUTHORS   Biggel,M.
  TITLE     Florfenicol-resistant Enterococci from pet food
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5254)
  AUTHORS   Biggel,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-MAY-2022) Institute for Food Safety and Hygiene,
            University of Zurich, Winterthurerstrasse 272, Zurich 8057,
            Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x, 100x
            Sequencing Technology :: Illumina MiniSeq, Oxford Nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_023299805.1-RS_2024_05_19
            Annotation Date                   :: 05/19/2024 04:32:28
            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)                     :: 2,710
            CDSs (total)                      :: 2,619
            Genes (coding)                    :: 2,507
            CDSs (with protein)               :: 2,507
            Genes (RNA)                       :: 91
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 69
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 112
            CDSs (without protein)            :: 112
            Pseudo Genes (ambiguous residues) :: 0 of 112
            Pseudo Genes (frameshifted)       :: 47 of 112
            Pseudo Genes (incomplete)         :: 50 of 112
            Pseudo Genes (internal stop)      :: 37 of 112
            Pseudo Genes (multiple problems)  :: 19 of 112
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP097065.1.
            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..5254
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /strain="AT02"
                     /isolation_source="pet food (BARF)"
                     /db_xref="taxon:1352"
                     /plasmid="pAT02-d"
                     /collection_date="2022"
                     /collected_by="ILS, University of Zurich"
     gene            complement(join(5181..5254,1..343))
                     /locus_tag="M2900_RS13445"
                     /old_locus_tag="M2900_13440"
     CDS             complement(join(5181..5254,1..343))
                     /locus_tag="M2900_RS13445"
                     /old_locus_tag="M2900_13440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001232859.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002305824.1"
                     /translation="MRKTSVQKHVTLYPSHVDVLDSIIEKNPDVNNYSEAIRFLCMSYE
                     PDTNTTTTSNQAKLNAMGKEISIMTEIMAEFADLYLKDTGVLIGTNSKVYQEVKEKIEN
                     QLNPSRRNQPKNRQKETNQTFTSGNFDPTNFLKR"
                     /name="hypothetical protein"
     gene            complement(345..626)
                     /locus_tag="M2900_RS13450"
                     /old_locus_tag="M2900_13445"
     CDS             complement(345..626)
                     /locus_tag="M2900_RS13450"
                     /old_locus_tag="M2900_13445"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000353845.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000353845.1"
                     /translation="MDILVRNINPKIITRIDKRCQELTTKTGKKWSRNQYLKILIENDF
                     DHELMNYKKDQFDLLFEKFIAIQAENTNILNDYVHTNNQLIETLIGGI"
                     /name="hypothetical protein"
     gene            complement(1002..1526)
                     /locus_tag="M2900_RS13455"
                     /old_locus_tag="M2900_13450"
     CDS             complement(1002..1526)
                     /locus_tag="M2900_RS13455"
                     /old_locus_tag="M2900_13450"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002305828.1"
                     /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_002305828.1"
                     /translation="MTEKTIKELAEELGVSKTAINKKVSDENRKLWFSKIGNKFVINET
                     GQKAIKSMFFNENENSNQQLVGEKTKTENHKNANQVPELEVLSLLEQQLNQKDMQLQEK
                     DEQIKQMQKLLDQQQQLTLQANQQIEKLQEQLQLTYTEESSENKSTTLSEETESIEKQS
                     KTEKKWWQFWQ"
                     /name="DUF536 domain-containing protein"
     gene            complement(1543..2511)
                     /locus_tag="M2900_RS13460"
                     /old_locus_tag="M2900_13455"
     CDS             complement(1543..2511)
                     /locus_tag="M2900_RS13460"
                     /old_locus_tag="M2900_13455"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002332718.1"
                     /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_002332718.1"
                     /translation="MANEIVKYHHELNTIPLRKFTSVEMNLFFSIVSRMRDVGDKKVQF
                     TFEQLKDLSNYKATANVRFIDDLETTYDKLMDLRFGRRSADGLQRERFVLFNQFKIDGK
                     ADIPFAEIQVHEKALPLLNNLEEWVRYSLQQFNELESSYSKTMFRLLKQYRTKGIAYFS
                     KEDFHELLDIPKSYRESDINKKIIKPIRQELTAIFKGLTIQKRYGKGRGKPVIGYQFTF
                     KPEIKKSDDFNKHAPTKEEQNKALELANQQVQSEKAPTSLQEKIKEQKRKLELLQQLEK
                     LEREQNTQNKENNAQKSEINSDIPSELKKDLLDNLQNLFKD"
                     /name="replication initiation protein"
     gene            3660..4679
                     /locus_tag="M2900_RS13465"
                     /old_locus_tag="M2900_13460"
     CDS             3660..4679
                     /locus_tag="M2900_RS13465"
                     /old_locus_tag="M2900_13460"
                     /inference="COORDINATES: protein motif:HMM:NF019371.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Abi family protein"
                     /protein_id="WP_010729551.1"
                     /translation="MKTSNRKYKVKTVNHRIPPKKALCVINNSKVINQELKPYLSEQEM
                     IKKISKDIFLTNSDTILLEKFLKKNSYFRFSIYVKLMKNIDKVTILDVIETYKLDSFIR
                     NQLHYFVNQIEIFWKKSLSDNMCVSYEETSIFPKNQCYLDKNIYSDLKWAEDIIGHFNS
                     FFYSNQSPTFKHHHIKKNHCLPIWALFEEITFGSLTTFINQLNTEYYNNWVMSCYDNPK
                     YKKAIRSWANVIRAYRNKIAHHSRIYAFKVTDAPTIIKNDSKSYFPENNLKETQKLYLY
                     GGLYVIKHLLIYEDSMTQTLWNKFLIDLEKKIDKIPSLEKSNYGFPENWRNKLKIMIV"
                     /name="Abi family protein"
     Typing          complement(1548..2511)
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.764"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 tgggttgatt tcgtcgggaa ggattgagtt gattttcaat tttttctttc acttcttgat
       61 atactttaga atttgtaccg ataagaacac cagtatcttt tagatataaa tcagcaaatt
      121 ctgccatgat ttctgtcatg atagaaattt cttttcccat ggcattgagt tttgcttggt
      181 tactggttgt ggttgtattg gtatcaggtt cataactcat acataaaaag cgaatggctt
      241 ctgaataatt gttaacgtct ggattttttt cgatgatgga atctaaaacg tcaacgtgac
      301 tgggataaag ggttacgtgt ttttgaacag aagtttttct catgttatat tcctccgata
      361 agtgtttcaa tgagttggtt gtttgtgtga acatagtcat ttagtatgtt cgtattttct
      421 gcttgaatgg caataaattt ttcgaataat aaatcgaatt gatctttttt gtaattcata
      481 agttcgtggt caaaatcgtt ttcgattaaa atttttaggt attgatttcg actccatttt
      541 ttgcccgttt tggttgttag ttcctgacaa cgtttatcta ttcttgtaat aattttggga
      601 ttgatatttc gaactaaaat gtccatggaa attttccttt cgtatcagtg tataatttat
      661 gtatatcata caaatatagt atttgtatag ctatttttcg ccaaaacact atacatagcc
      721 tagccacaat ggcaaaaaag tgatagcaaa tttttttctg agaaacgtga taggcacagc
      781 ttatctagca cctttcgtaa gaaagtgata ccacgtttcc ttatgctctt tcaaaattca
      841 gaaaaatcag ctgtaaaacg agtgcagtcc gagtaagatt caacgaaaaa acggggattg
      901 gggcgccacc aaaatatcgc aacatgggcc catgttgctc tgctcgcaaa agaaaaaaga
      961 agaataaaac cagcaatttt tattaattta aattgctggt tttattgcca gaattgccac
     1021 cattttttct ccgtctttga ttgtttttct atcgattctg tttcttcaga aagagtcgtt
     1081 gatttatttt ccgaagattc ttccgtataa gtcaactgta gttgttcctg cagtttctcg
     1141 atttgttggt tggcttgcag ggtgagttgt tgttgttggt cgagtaattt ttgcatttgt
     1201 tttatttgct cgtctttttc ttgtagttgc atatcttttt gatttaactg ttgttctagg
     1261 agagaaagga cttctaattc gggaacttgg ttggcgtttt tgtggttttc ggttttagtt
     1321 ttttcgccaa ctagttgttg atttgagttt tcgttttcgt taaaaaacat tgattttata
     1381 gccttttgtc cggtttcatt aatcacaaac ttgtttccga ttttcgaaaa ccaaagtttt
     1441 cgattttcgt cagaaacttt tttgttaatt gctgttttac taactcctaa ttcttcagca
     1501 agttctttga ttgttttttc tgtcataaaa tctaaaaacc cctcaatctt tgaataagtt
     1561 ttgaagattg tctaataagt ctttttttag ttctgaagga atatcggaat ttatctctga
     1621 tttttgtgca ttattttctt tattttgggt attttgttct ctttctaact tttctaactg
     1681 ttgtaaaagt tccaattttc gcttttgttc tttgattttt tcttgtaatg aagtaggtgc
     1741 tttttcagat tgaacttgtt ggttagctag ttctaatgct ttgttttgtt cttcttttgt
     1801 tggggcatgt ttgttaaagt cgtctgattt ttttatctca ggtttaaatg taaattgata
     1861 gccaatgaca ggctttcccc gtccttttcc gtatctcttt tggattgtca gacctttgaa
     1921 gattgcggtt agttcttggc gaataggctt tataattttt ttatttatat cactttctct
     1981 ataactttta gggatatcaa gtaattcatg aaagtcttct tttgaaaaat aggcaattcc
     2041 tttggttctg tattgtttta ataatctaaa catggttttg gaataactgc tttctaattc
     2101 attgaattgt tggagagaat atcgaaccca ttcttcaaga ttattaagta agggtaaggc
     2161 tttctcatgg acttgtattt cagcaaaagg aatatcagct tttccatcga ttttaaattg
     2221 attaaataaa acaaatcgtt cacgttgcaa accgtcagca cttcttctac caaaacgtaa
     2281 atccattaat ttgtcatacg ttgtttctaa atcatctatg aatcgaacat ttgcagttgc
     2341 tttataattg cttaaatctt ttaattgttc gaatgtaaat tgtacttttt tatcgcctac
     2401 gtcacgcatt ctagatacta tagagaagaa taaattcatt tctactgacg taaatttgcg
     2461 taaaggaatc gtatttaatt catggtggta tttcacaatt tcatttgcca taaaatcctc
     2521 cttcaagatt aactacttaa caaaattata aagagctttc taataggggt caagccccta
     2581 attaaagacc cctaaaaaca gacaaaaaga cccccaaaaa cagacaaaaa gacccctaaa
     2641 aacagacaaa aagaccccta aaaacagaca aaaagacccc caaaagattc tgcacacctt
     2701 gggagagtaa gcatacagcc gacggtaaag aggtttaaaa agaggtttaa aaagagatta
     2761 taaaagagga gaggggcaaa atttcccgcc taaaaatttt ctgctttttt agccaaacag
     2821 gttcgcgaat tttactaaac tgggaaactt gctccctctg gtcgctaaaa aggtgtgagg
     2881 gaaaaacacc ctcacattgt acctgcgcag tcgcctaaag gctcctttgc taaaaacgtt
     2941 gtttaaagag atttttttag aggctctgcg cgctcgttta agccgtttta agacagttta
     3001 gtatggataa cccttatctt gttcttaaag caccttacag gcggtcaggg caagccctaa
     3061 caacccttaa agagcataaa accatcctaa aattcgattt aatctgtctt atctatgttc
     3121 ttgtatattt tatatacctt gggtagtaaa acgtctgaaa acgcaaataa gagcgtatga
     3181 aacaaaacaa taagcaaccg attcagcaga attccggagg agccattttc gtacgttagc
     3241 aaaaaagtgc tgttgctaaa agctgcttgc ggtgcggagc gaacaaggtc tcctagagcg
     3301 agacgtgtac aaacaagctt acaaattcgt gaaaggcacc ggttttgcgc catttccaag
     3361 caaaaaaagg tctatcgagc ttgctcgata gaccgatcgc atttagcccc ccgcattcta
     3421 acaggggggg aataatgtga aaaattatgg tagtaatgct tgatatatag gcatttcttt
     3481 tggttgcaca cttaaaaaaa atcacgattt tgacaactaa atttttaaat aaaaaagctt
     3541 tacagtttaa ttcaaatgtg ttttaatata tctatcagta cttgccacgc ctctgattta
     3601 atatcatgcg cattatggta gggctttttt tttatatttt tttaagaaag aagattctta
     3661 tgaagacatc aaatagaaaa tataaagtta aaacagttaa tcatagaatt ccacctaaaa
     3721 aggcattatg tgtaattaat aattccaaag taattaatca agagttaaaa ccatatttat
     3781 ccgagcaaga aatgataaaa aaaataagta aagatatttt tttaacaaat tccgatacaa
     3841 ttttattaga aaagttttta aagaaaaata gttattttcg atttagtatt tatgttaaat
     3901 taatgaaaaa tatagataaa gttactattc tagatgttat tgaaacgtac aaattagatt
     3961 cattcattcg taatcaattg cattattttg tgaatcaaat agaaattttt tggaaaaaat
     4021 ctctttcaga taatatgtgc gtttcttatg aagaaactag catatttccg aagaatcagt
     4081 gttatttgga taaaaatatt tattcagatt tgaaatgggc tgaagatata attggtcatt
     4141 ttaatagttt tttttattca aatcaaagtc ccacttttaa acatcatcat ataaaaaaaa
     4201 atcattgttt accaatatgg gctttatttg aagaaataac atttggtagt ttaacaacat
     4261 ttattaatca acttaataca gagtattata ataattgggt catgagctgt tatgataatc
     4321 ctaaatacaa aaaagctata cgaagttggg caaacgtaat tagagcttat agaaataaga
     4381 tagctcatca ttcaagaata tatgcattta aagttactga cgctccaaca atcataaaaa
     4441 atgattccaa aagttatttt cctgaaaata acttaaaaga aacccaaaag ttatatttgt
     4501 atggaggatt atacgttata aaacatctgt taatatatga agatagcatg acacaaactt
     4561 tatggaataa atttctaata gatttagaaa aaaagatcga taaaatccct tccttagaaa
     4621 aatccaatta tggttttccg gaaaattgga gaaacaagtt aaaaataatg attgtttaat
     4681 tgttatttaa attgttagta gacataatgt atatactacc aagtagcccc tggatcaacc
     4741 gatccagggg aagactttgt gattttcaat tggtctatct aaaacatctt tttaaaagct
     4801 tgattcttcg ctgttggctt ttttcgattc tttgtgaata ttcagtgatt atttttttac
     4861 tacttgttat tttccgaggg atttgttaaa agtttaatag cgtttctcag taagggacgt
     4921 cgttttttca ttttcctatg tatggactgc tcgaacgagc agcctttttt tattccaggg
     4981 aacgtcctat tctttgagtt tccatgctat tgaataaccg ggacttaggg attagggcag
     5041 cgccccaaaa tgaaaaaaga aaaatccgct tctgcgaatt cttctttttt ttcgcaagtt
     5101 ggtaccaact tgcaaatctt gctggaagac cgatccctaa aaagaaatcg aggaattttt
     5161 ttgtttttcg gtttcttttt ttatcttttt agaaagtttg ttgggtcaaa atttccagaa
     5221 gtaaaggttt gattggtttc tttttgacga tttt
//
