LOCUS       NZ_LR135361             5779 bp    DNA     linear   CON 13-FEB-2024
DEFINITION  Enterococcus faecium isolate E7948 plasmid 5.
ACCESSION   NZ_LR135361
VERSION     NZ_LR135361.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMEA4885488
            Assembly: GCF_900639585.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 5779)
  AUTHORS   Arredondo-Alonso,S.
  TITLE     Direct Submission
  JOURNAL   Submitted (21-DEC-2018) UNIVERSITY MEDICAL CENTER UTRECHT,
            Heidelberglaan 100, 3584 CX Utrecht, Netherlands
COMMENT     ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/13/2024 02:54:30
            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)                     :: 2,980
            CDSs (total)                      :: 2,889
            Genes (coding)                    :: 2,768
            CDSs (with protein)               :: 2,768
            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)              :: 121
            CDSs (without protein)            :: 121
            Pseudo Genes (ambiguous residues) :: 0 of 121
            Pseudo Genes (frameshifted)       :: 53 of 121
            Pseudo Genes (incomplete)         :: 66 of 121
            Pseudo Genes (internal stop)      :: 32 of 121
            Pseudo Genes (multiple problems)  :: 24 of 121
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            LR135361.1.
            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/
FEATURES             Location/Qualifiers
     source          1..5779
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /isolate="E7948"
                     /db_xref="taxon:1352"
                     /plasmid="5"
     gene            <1..546
                     /locus_tag="EQB40_RS15555"
     CDS             <1..546
                     /locus_tag="EQB40_RS15555"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002338009.1"
                     /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_164853351.1"
                     /translation="SYSKTMFRLLKQYRTKGIANFSKEDFHELLDIPKSYRESDINKKI
                     IKPIRQELTAIFKGLTIQKRYGKGRGKPVIGYQFTFKPEIKKSDDFNKHAPTKEEQNKA
                     LELANQQVQSEKEPTSLQEKIKEQKRKLELLQQLAELERKQNTPSKKINKQIADNNSDI
                     TPEFKENLLDNLQNLFKE"
                     /name="replication initiation protein"
     gene            556..1044
                     /locus_tag="EQB40_RS15560"
     CDS             556..1044
                     /locus_tag="EQB40_RS15560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002347002.1"
                     /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_060763418.1"
                     /translation="MTDKTIKELADILGVSKDKVKYQLRKLPSNFTYKKGNITYLKKEA
                     VTTITKVLSGNESGNLPSELPDSLPTDYLLKEIETKNNHIEEKDRQIEKLQIALETQQK
                     LLDQQQQLTLQANQQIKKLHEQLQLTYAEESSEKEPLSVTEETQKGQNKEKKWWQFWQ"
                     /name="DUF536 domain-containing protein"
     gene            1340..1621
                     /locus_tag="EQB40_RS15565"
     CDS             1340..1621
                     /locus_tag="EQB40_RS15565"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002296853.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002368064.1"
                     /translation="MDILVRNIDPKVISEIDRRCQELTTKTGKKWSRNAYLKVLIENDF
                     DQALRHYKKDQFDLLLEKFIDIQAKNTETLNDYVHTNNQLIETLIGGI"
                     /name="hypothetical protein"
     gene            1623..2039
                     /locus_tag="EQB40_RS15570"
     CDS             1623..2039
                     /locus_tag="EQB40_RS15570"
                     /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_002368067.1"
                     /translation="MRKTSVQKHVTLYPSHIDVLDSIIEKNPDINNYSEAIRFLCMSYE
                     PNTNTTTTSNQAKLNAMGKEISIMSEIIAEFADLYLKDTGVLIGTNSKVYQEVKEKIEN
                     QLNPSRRNQPKNRQKETNQTFTSRNFDPTNFLKR"
                     /name="hypothetical protein"
     gene            2653..3807
                     /locus_tag="EQB40_RS15575"
     CDS             2653..3807
                     /locus_tag="EQB40_RS15575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002348970.1"
                     /GO_function="GO:0008234 - cysteine-type peptidase activity
                     [Evidence IEA]"
                     /GO_process="GO:0006508 - proteolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="C47 family peptidase"
                     /protein_id="WP_060763417.1"
                     /translation="MIILKPKKKIYLGLLFSLMIGIFSIGITNTYASENSNFNINSQPI
                     EEQAINFAKTDFEHSITSILLMENNTETDINYTLGSPFKMLDGENTANSSIFFPVFSDA
                     DNTIKYIYTVKKNTNGEYSGSISQFLAKELQNLVDSNITDTTLFFQDNSIYYSDNGQIK
                     LLWKSPLSTEKNGVSSLTEKNDLISVNIKNKIKNFSKKQNFPAVKRVKSVSSGDNFIMI
                     NWRIAETQTSFPWCAAYVEAAILCNKTDVRATSARAIMHYTYPNLNNSQIESKSLNQDQ
                     IIKYANYCGVYPKKIARILNLSEVQTQLRKGNAIYMGTAGYGNYSNSRHALALFGWVNQ
                     GGYQTYYVWNPWYNYPTVISANAGPVTIPVPGGGFTWDNTITNW"
                     /name="C47 family peptidase"
     gene            3780..4223
                     /locus_tag="EQB40_RS15580"
     CDS             3780..4223
                     /locus_tag="EQB40_RS15580"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002334327.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_223917876.1"
                     /translation="MGQYHYKLVNKLIALVMGLVLVLFLTSCSKKQEIQKTDLIPFLGT
                     WQTKDHSERLVITNLNTSKNIEQYTILVKENNHKIQIIDKNLNINEQVFIYKATNNLLT
                     LRSNKKQLDYTFSLDSPKKLVFILTTNDGTEGTAKPIEFFKAD"
                     /name="hypothetical protein"
     gene            4524..>4669
                     /locus_tag="EQB40_RS16090"
                     /pseudo=""
     CDS             4524..>4669
                     /locus_tag="EQB40_RS16090"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002348702.1"
                     /note="frameshifted; internal stop; incomplete; partial in
                     the middle of a contig; missing C-terminus; Derived by
                     automated computational analysis using gene prediction
                     method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization relaxosome protein MobC"
                     /name="plasmid mobilization relaxosome protein MobC"
     gene            5357..>5779
                     /locus_tag="EQB40_RS15590"
     CDS             5357..>5779
                     /locus_tag="EQB40_RS15590"
                     /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_164853352.1"
                     /translation="MANEIVKYHHELNTIPLRKFTSVEMNLFFSIISRMRDVGDKKVQF
                     TFEQLKDLSNYKATANVRFIDDLETTYDKLMDLRFGRRSADGLQRERFVLFNQFKIDGK
                     ADIPFAEIQVHEKALPLLNNLEEWVRYSLQQFNELES"
                     /name="replication initiation protein"
     Typing          2..546
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.007"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          5358..5779
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agttattcca aaaccatgtt tagattatta aaacaataca gaaccaaagg aattgccaat
       61 ttttcaaaag aagactttca tgaattactt gatatcccta aaagttatag agaaagtgat
      121 ataaataaaa aaattataaa gcctattcgc caagaactaa ccgcaatctt caaaggtttg
      181 acaatccaaa agagatacgg aaaaggacgg ggaaagcctg tcattggcta tcaatttaca
      241 tttaaacctg agataaaaaa atcagacgac tttaacaaac atgctccaac caaagaagaa
      301 caaaataaag ctttggaact agctaatcaa caggttcaat ctgaaaaaga acctacttca
      361 ttacaagaaa aaatcaaaga acaaaaacga aaattagaac ttttacaaca gttagcagaa
      421 ttagaaagaa aacaaaatac cccaagtaag aaaattaaca aacaaatagc agataacaat
      481 tccgatatta ccccagaatt taaagaaaac ttactagata atctccaaaa cttatttaaa
      541 gaataagggg tttttatgac agataaaact atcaaagaat tagcagatat tctaggtgtt
      601 tcaaaagata aagtgaagta tcaactgagg aaattaccta gtaattttac ctacaaaaaa
      661 ggaaatatta cctacctgaa aaaagaagca gtaacaacaa ttacaaaggt tttatcaggt
      721 aatgaatcgg gtaacttacc tagtgaatta cccgattcat tacctaccga ttacctactc
      781 aaggagattg aaactaagaa taatcatatt gaagaaaaag ataggcaaat tgaaaaactt
      841 caaatagctt tagaaacgca gcaaaaatta ctcgaccagc aacaacaact caccctacaa
      901 gccaatcaac aaatcaaaaa acttcacgaa caactccagc taacctatgc agaagaatct
      961 tcagaaaaag aacccctttc tgttactgaa gaaactcaaa aaggacaaaa caaggagaaa
     1021 aaatggtggc aattctggca ataacccaac aatttttatt cataaaaatt gttgggttac
     1081 tttctttttt tgcttttaca agcatagcga catgatctca cgtcgctatt ttttaaagag
     1141 cataaggaaa cgcggtatca ctttcttacg aaaggtgcta ggtaggctgt gcctaccacg
     1201 tttctaagaa aaaaatttgc tatcactttt tcgtcattgt ggatagctta tgtatagtgt
     1261 ttcggcaaaa aacagctata caaatactat atttgtatga tatacataaa ttatacacaa
     1321 atgcgaaagg aattcttcta tggacatttt agttcggaat attgatccaa aagttatttc
     1381 agaaatagat agacgttgcc aagaactcac aacaaaaact ggcaaaaaat ggagccgtaa
     1441 tgcgtaccta aaagttctaa tcgaaaacga ttttgaccag gcacttaggc attacaaaaa
     1501 agatcaattc gatttattac tcgaaaaatt tatcgatata caagcaaaaa atactgaaac
     1561 attgaacgac tatgttcata caaacaacca actcattgaa acacttatcg gaggaatata
     1621 acatgagaaa aacttctgtt caaaaacacg ttacccttta tcccagtcac attgacgttt
     1681 tagattccat catcgaaaaa aatccagata tcaataacta ctcggaagcc attcgttttc
     1741 tatgtatgag ttatgaacct aatactaata cgacaactac cagcaaccaa gcaaaactaa
     1801 atgcgatggg aaaagaaatt tctattatgt ccgaaatcat tgcagaattt gctgatttat
     1861 atctaaaaga tactggtgtt cttatcggta caaattctaa agtatatcaa gaagtgaaag
     1921 aaaaaattga aaatcaactc aatccctccc gacgaaatca acccaaaaat cgtcaaaaag
     1981 aaaccaatca aacattcact tctagaaatt ttgacccaac aaactttcta aaaagatgaa
     2041 aaagaaaccg aaaatttttt ctatttctca gtttcttttt tagggggcag tcttccagca
     2101 agatttgcaa gttaccggta acttgcacaa aaaaagaaaa atccgcttgt gcgaatcctt
     2161 ctttttgcat tttggggcgc tgccccaatc tccaaatatc ggttatttaa tagcgtggta
     2221 actcaaaaaa atagaacgta ctctgaaata aaaaaagact gctctaacga gcagccaata
     2281 aaaaataatg agcgtttatt cttgaaaaag cagcgcgctt atgaagcgct gccaaaaatt
     2341 taccatattt tatgaaaaat aacaagtttc taaaaaggaa tcggttaaga ttcacaaaga
     2401 atcgtaaaca gacaatagcg gaaaatcaag cttccgaacg taccttttag ctagaccaat
     2461 gaaaaatcac aaagtgagcg gctggatcgg ttggtacagg ggctacttgg catagtcgac
     2521 attatgttaa ctaacgctat aaataacgat tatgttccca aaacaatatt ttatgaacta
     2581 taacaaaaat ttgttatcgc atattgtata ttttaattat aggtgtatac cacttaaatt
     2641 taacacaaag gcgtgattat tttgaaaccc aaaaagaaaa tttatctagg tctcctcttt
     2701 tccttgatga ttggaatttt tagtatagga attacaaata cctatgcttc agaaaattct
     2761 aatttcaata tcaactccca accaattgaa gaacaagcaa ttaattttgc gaaaactgat
     2821 tttgaacact ccataacttc aattctttta atggaaaata acaccgaaac tgatattaac
     2881 tatactcttg gttcgccatt taaaatgctc gatggagaaa atacggcaaa tagttctatt
     2941 ttctttccag tattttcaga cgctgataat acgattaaat atatttatac cgtcaaaaaa
     3001 aatacaaatg gagaatattc aggaagtatt tcacaatttt tagcaaaaga acttcaaaat
     3061 ctagtagata gtaatataac agatacaacc ttattttttc aagataatag catttattat
     3121 tccgataatg gacaaattaa actactttgg aaatcacctt taagtacaga aaaaaatggt
     3181 gtttcttccc ttacagaaaa aaatgatctt atatccgtaa atataaaaaa taaaattaaa
     3241 aatttttcta aaaaacaaaa ttttcctgcg gttaaacgtg taaaaagtgt ctcctccgga
     3301 gataacttta ttatgattaa ttggcgtata gcagaaaccc aaacaagttt tccgtggtgc
     3361 gctgcttacg tagaagctgc tatcttatgt aacaaaacag atgtacgtgc tacttcagct
     3421 agagccatta tgcattatac ctatcctaat ttaaacaaca gtcaaattga atcaaaaagt
     3481 cttaatcaag atcaaataat aaaatatgca aattactgtg gtgtttatcc taaaaaaata
     3541 gcacgaatac taaacctttc agaggtccaa acacaactaa gaaaaggaaa tgccatttat
     3601 atgggaactg ctggttatgg aaattatagt aacagccgtc atgcacttgc attatttggg
     3661 tgggtcaatc aaggtggtta tcaaacttac tatgtgtgga atccttggta taactaccca
     3721 actgtaataa gtgcaaatgc aggaccagtt acaattcctg tacctggagg tggttttact
     3781 tgggacaata ccattacaaa ttggtaaata aactcattgc tttagttatg ggtctagtgt
     3841 tagttctttt cttaactagt tgttcaaaaa aacaagaaat acaaaagact gatctgattc
     3901 cttttctagg aacttggcaa actaaagatc attcagaacg tctagtaatc actaatttaa
     3961 atacttcaaa aaatatagaa caatatacca tcttagtaaa agagaacaat cataaaattc
     4021 aaatcattga taaaaattta aatataaatg aacaagtttt catttacaaa gcaacaaata
     4081 atttactaac actgcgctcg aataaaaaac aattagatta cacttttagt ttggattctc
     4141 caaaaaagct cgtatttatt ttgacaacga atgatgggac agaagggaca gctaaaccaa
     4201 ttgaattttt taaagctgat tgatgaatag ttgtttgata ttacaaaaca ataatttcac
     4261 cgaaggtgaa acaagcgaaa ctttacaaaa agtggctagc atttgctagc cttttttgta
     4321 ttgtggagcg tgggttttga gggggattca agggggagct tgcgcccctt tgacaagcgg
     4381 ttatttgcac caaatacgta ggtatttggc tagcaaatat agagcttgcc aagcccttta
     4441 gtgtgttttg tagaaaggga ccttatagtc actttcacat tacaaacgat acgtccatag
     4501 gacgtatcaa aagggtggga cttatgagca aattaaagca aaatttggct agcaatcctt
     4561 ctaaaaaata cacctattga tcagagtcaa aataaatcag ttttcgagtg agcgaatcca
     4621 aatttgcaac tctgaagctt tgcaaatgag tgtgccggct tccgtaaaag tctaggtaac
     4681 attagtcgat atatacatag ggctctaatt tgcgttttaa ggcgttttaa acgttctggt
     4741 atgtaattat accaaagcga ctttaaaacg ccttaaaacg aattttagag gttctgtaga
     4801 acgttttagg gttgttaggg cttgccctga ccgcctgtaa ggcgctttaa aaacaagata
     4861 agggatttta tctagacttg tcttaaaacg ccgtagatga gcgctcagag cttctaaaag
     4921 gactccttac gaactgtttt taagcaaagg agcctttagg cgactgcgca gtttaatgtg
     4981 agagcgtagc gatcacacct ttaaagcgac cgtagggagc agattcccag tttaggaaat
     5041 ttcgcgaacc tgtttggaga aaaaaagtag gaaaatttta ggcgggaaat tttgcccccc
     5101 tcttttataa tctcttttat aacctctttt taaacctctt taccgtcggc tgtatcctta
     5161 ctctcccaag gtgtgcagaa tcttttaggg gtctttttgt ctgtttttag gggtcttttt
     5221 gtctgttttt aggggtcttt ttgtctgttt ttaggggtct ttttgtctgt ttttaggggt
     5281 ctttaattag ggggttgacc cccattagaa agctctttat aattttgtta agtagttaat
     5341 cttgaaggag gattttatgg caaatgaaat tgtgaaatac caccatgaat taaatacgat
     5401 tcctttacgc aaatttacgt cagtagaaat gaatttattc ttctctataa tatctagaat
     5461 gcgtgatgta ggcgataaaa aagtacaatt tacattcgaa caattaaaag atttaagcaa
     5521 ttataaagca actgcaaatg ttcgattcat agatgattta gaaacaacgt atgacaaatt
     5581 aatggattta cgttttggta gaagaagtgc tgacggtttg caacgtgaac gatttgtttt
     5641 atttaatcaa tttaaaatcg atggaaaagc tgatattcct tttgctgaaa tacaagtcca
     5701 tgagaaagcc ttacccttac ttaataatct tgaagaatgg gttcgatatt ctctccaaca
     5761 attcaatgaa ttagaaagc
//
