LOCUS       NZ_LR135424             5779 bp    DNA     linear   CON 01-JUN-2024
DEFINITION  Enterococcus faecium isolate E8440 plasmid 6.
ACCESSION   NZ_LR135424
VERSION     NZ_LR135424.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMEA4885812
            Assembly: GCF_900639645.1
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 Name                   :: GCF_900639645.1-RS_2024_06_01
            Annotation Date                   :: 06/01/2024 05:45:23
            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)                     :: 3,282
            CDSs (total)                      :: 3,190
            Genes (coding)                    :: 3,081
            CDSs (with protein)               :: 3,081
            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)              :: 109
            CDSs (without protein)            :: 109
            Pseudo Genes (ambiguous residues) :: 0 of 109
            Pseudo Genes (frameshifted)       :: 34 of 109
            Pseudo Genes (incomplete)         :: 66 of 109
            Pseudo Genes (internal stop)      :: 28 of 109
            Pseudo Genes (multiple problems)  :: 15 of 109
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            LR135424.1.
            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="E8440"
                     /db_xref="taxon:1352"
                     /plasmid="6"
     gene            <1..318
                     /locus_tag="FQ475_RS16240"
     CDS             <1..318
                     /locus_tag="FQ475_RS16240"
                     /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_284166683.1"
                     /translation="SEAIRFLCMSYEPNTNTTTTSNQAKLNAMGKEISIMSEIIAEFAD
                     LYLKDTGVLIGTNSKVYQEVKEKIENQLNPSRRNQPKNRQKETNQTFTSRNFDPTNFLK
                     R"
                     /name="hypothetical protein"
     gene            932..2086
                     /locus_tag="FQ475_RS16245"
     CDS             932..2086
                     /locus_tag="FQ475_RS16245"
                     /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            2059..2502
                     /locus_tag="FQ475_RS16250"
     CDS             2059..2502
                     /locus_tag="FQ475_RS16250"
                     /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            2803..>2948
                     /locus_tag="FQ475_RS16255"
                     /pseudo=""
     CDS             2803..>2948
                     /locus_tag="FQ475_RS16255"
                     /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            3636..4604
                     /locus_tag="FQ475_RS16260"
     CDS             3636..4604
                     /locus_tag="FQ475_RS16260"
                     /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_002368293.1"
                     /translation="MANEIVKYHHELNTIPLRKFTSVEMNLFFSIISRMRDVGDKKVQF
                     TFEQLKDLSNYKATANVRFIDDLETTYDKLMDLRFGRRSADGLQRERFVLFNQFKIDGK
                     ADIPFAEIQVHEKALPLLNNLEEWVRYSLQQFNELESSYSKTMFRLLKQYRTKGIANFS
                     KEDFHELLDIPKSYRESDINKKIIKPIRQELTAIFKGLTIQKRYGKGRGKPVIGYQFTF
                     KPEIKKSDDFNKHAPTKEEQNKALELANQQVQSEKEPTSLQEKIKEQKRKLELLQQLAE
                     LERKQNTPSKKINKQIADNNSDITPEFKENLLDNLQNLFKE"
                     /name="replication initiation protein"
     gene            4614..5102
                     /locus_tag="FQ475_RS16265"
     CDS             4614..5102
                     /locus_tag="FQ475_RS16265"
                     /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            5398..5679
                     /locus_tag="FQ475_RS16270"
     CDS             5398..5679
                     /locus_tag="FQ475_RS16270"
                     /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"
     Typing          3637..4604
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tcggaagcca ttcgttttct atgtatgagt tatgaaccta atactaatac gacaactacc
       61 agcaaccaag caaaactaaa tgcgatggga aaagaaattt ctattatgtc cgaaatcatt
      121 gcagaatttg ctgatttata tctaaaagat actggtgttc ttatcggtac aaattctaaa
      181 gtatatcaag aagtgaaaga aaaaattgaa aatcaactca atccctcccg acgaaatcaa
      241 cccaaaaatc gtcaaaaaga aaccaatcaa acattcactt ctagaaattt tgacccaaca
      301 aactttctaa aaagatgaaa aagaaaccga aaattttttc tatttctcag tttctttttt
      361 agggggcagt cttccagcaa gatttgcaag ttaccggtaa cttgcacaaa aaaagaaaaa
      421 tccgcttgtg cgaatccttc tttttgcatt ttggggcgct gccccaatct ccaaatatcg
      481 gttatttaat agcgtggtaa ctcaaaaaaa tagaacgtac tctgaaataa aaaaagactg
      541 ctctaacgag cagccaataa aaaataatga gcgtttattc ttgaaaaagc agcgcgctta
      601 tgaagcgctg ccaaaaattt accatatttt atgaaaaata acaagtttct aaaaaggaat
      661 cggttaagat tcacaaagaa tcgtaaacag acaatagcgg aaaatcaagc ttccgaacgt
      721 accttttagc tagaccaatg aaaaatcaca aagtgagcgg ctggatcggt tggtacaggg
      781 gctacttggc atagtcgaca ttatgttaac taacgctata aataacgatt atgttcccaa
      841 aacaatattt tatgaactat aacaaaaatt tgttatcgca tattgtatat tttaattata
      901 ggtgtatacc acttaaattt aacacaaagg cgtgattatt ttgaaaccca aaaagaaaat
      961 ttatctaggt ctcctctttt ccttgatgat tggaattttt agtataggaa ttacaaatac
     1021 ctatgcttca gaaaattcta atttcaatat caactcccaa ccaattgaag aacaagcaat
     1081 taattttgcg aaaactgatt ttgaacactc cataacttca attcttttaa tggaaaataa
     1141 caccgaaact gatattaact atactcttgg ttcgccattt aaaatgctcg atggagaaaa
     1201 tacggcaaat agttctattt tctttccagt attttcagac gctgataata cgattaaata
     1261 tatttatacc gtcaaaaaaa atacaaatgg agaatattca ggaagtattt cacaattttt
     1321 agcaaaagaa cttcaaaatc tagtagatag taatataaca gatacaacct tattttttca
     1381 agataatagc atttattatt ccgataatgg acaaattaaa ctactttgga aatcaccttt
     1441 aagtacagaa aaaaatggtg tttcttccct tacagaaaaa aatgatctta tatccgtaaa
     1501 tataaaaaat aaaattaaaa atttttctaa aaaacaaaat tttcctgcgg ttaaacgtgt
     1561 aaaaagtgtc tcctccggag ataactttat tatgattaat tggcgtatag cagaaaccca
     1621 aacaagtttt ccgtggtgcg ctgcttacgt agaagctgct atcttatgta acaaaacaga
     1681 tgtacgtgct acttcagcta gagccattat gcattatacc tatcctaatt taaacaacag
     1741 tcaaattgaa tcaaaaagtc ttaatcaaga tcaaataata aaatatgcaa attactgtgg
     1801 tgtttatcct aaaaaaatag cacgaatact aaacctttca gaggtccaaa cacaactaag
     1861 aaaaggaaat gccatttata tgggaactgc tggttatgga aattatagta acagccgtca
     1921 tgcacttgca ttatttgggt gggtcaatca aggtggttat caaacttact atgtgtggaa
     1981 tccttggtat aactacccaa ctgtaataag tgcaaatgca ggaccagtta caattcctgt
     2041 acctggaggt ggttttactt gggacaatac cattacaaat tggtaaataa actcattgct
     2101 ttagttatgg gtctagtgtt agttcttttc ttaactagtt gttcaaaaaa acaagaaata
     2161 caaaagactg atctgattcc ttttctagga acttggcaaa ctaaagatca ttcagaacgt
     2221 ctagtaatca ctaatttaaa tacttcaaaa aatatagaac aatataccat cttagtaaaa
     2281 gagaacaatc ataaaattca aatcattgat aaaaatttaa atataaatga acaagttttc
     2341 atttacaaag caacaaataa tttactaaca ctgcgctcga ataaaaaaca attagattac
     2401 acttttagtt tggattctcc aaaaaagctc gtatttattt tgacaacgaa tgatgggaca
     2461 gaagggacag ctaaaccaat tgaatttttt aaagctgatt gatgaatagt tgtttgatat
     2521 tacaaaacaa taatttcacc gaaggtgaaa caagcgaaac tttacaaaaa gtggctagca
     2581 tttgctagcc ttttttgtat tgtggagcgt gggttttgag ggggattcaa gggggagctt
     2641 gcgccccttt gacaagcggt tatttgcacc aaatacgtag gtatttggct agcaaatata
     2701 gagcttgcca agccctttag tgtgttttgt agaaagggac cttatagtca ctttcacatt
     2761 acaaacgata cgtccatagg acgtatcaaa agggtgggac ttatgagcaa attaaagcaa
     2821 aatttggcta gcaatccttc taaaaaatac acctattgat cagagtcaaa ataaatcagt
     2881 tttcgagtga gcgaatccaa atttgcaact ctgaagcttt gcaaatgagt gtgccggctt
     2941 ccgtaaaagt ctaggtaaca ttagtcgata tatacatagg gctctaattt gcgttttaag
     3001 gcgttttaaa cgttctggta tgtaattata ccaaagcgac tttaaaacgc cttaaaacga
     3061 attttagagg ttctgtagaa cgttttaggg ttgttagggc ttgccctgac cgcctgtaag
     3121 gcgctttaaa aacaagataa gggattttat ctagacttgt cttaaaacgc cgtagatgag
     3181 cgctcagagc ttctaaaagg actccttacg aactgttttt aagcaaagga gcctttaggc
     3241 gactgcgcag tttaatgtga gagcgtagcg atcacacctt taaagcgacc gtagggagca
     3301 gattcccagt ttaggaaatt tcgcgaacct gtttggagaa aaaaagtagg aaaattttag
     3361 gcgggaaatt ttgcccccct cttttataat ctcttttata acctcttttt aaacctcttt
     3421 accgtcggct gtatccttac tctcccaagg tgtgcagaat cttttagggg tctttttgtc
     3481 tgtttttagg ggtctttttg tctgttttta ggggtctttt tgtctgtttt taggggtctt
     3541 tttgtctgtt tttaggggtc tttaattagg gggttgaccc ccattagaaa gctctttata
     3601 attttgttaa gtagttaatc ttgaaggagg attttatggc aaatgaaatt gtgaaatacc
     3661 accatgaatt aaatacgatt cctttacgca aatttacgtc agtagaaatg aatttattct
     3721 tctctataat atctagaatg cgtgatgtag gcgataaaaa agtacaattt acattcgaac
     3781 aattaaaaga tttaagcaat tataaagcaa ctgcaaatgt tcgattcata gatgatttag
     3841 aaacaacgta tgacaaatta atggatttac gttttggtag aagaagtgct gacggtttgc
     3901 aacgtgaacg atttgtttta tttaatcaat ttaaaatcga tggaaaagct gatattcctt
     3961 ttgctgaaat acaagtccat gagaaagcct tacccttact taataatctt gaagaatggg
     4021 ttcgatattc tctccaacaa ttcaatgaat tagaaagcag ttattccaaa accatgttta
     4081 gattattaaa acaatacaga accaaaggaa ttgccaattt ttcaaaagaa gactttcatg
     4141 aattacttga tatccctaaa agttatagag aaagtgatat aaataaaaaa attataaagc
     4201 ctattcgcca agaactaacc gcaatcttca aaggtttgac aatccaaaag agatacggaa
     4261 aaggacgggg aaagcctgtc attggctatc aatttacatt taaacctgag ataaaaaaat
     4321 cagacgactt taacaaacat gctccaacca aagaagaaca aaataaagct ttggaactag
     4381 ctaatcaaca ggttcaatct gaaaaagaac ctacttcatt acaagaaaaa atcaaagaac
     4441 aaaaacgaaa attagaactt ttacaacagt tagcagaatt agaaagaaaa caaaataccc
     4501 caagtaagaa aattaacaaa caaatagcag ataacaattc cgatattacc ccagaattta
     4561 aagaaaactt actagataat ctccaaaact tatttaaaga ataaggggtt tttatgacag
     4621 ataaaactat caaagaatta gcagatattc taggtgtttc aaaagataaa gtgaagtatc
     4681 aactgaggaa attacctagt aattttacct acaaaaaagg aaatattacc tacctgaaaa
     4741 aagaagcagt aacaacaatt acaaaggttt tatcaggtaa tgaatcgggt aacttaccta
     4801 gtgaattacc cgattcatta cctaccgatt acctactcaa ggagattgaa actaagaata
     4861 atcatattga agaaaaagat aggcaaattg aaaaacttca aatagcttta gaaacgcagc
     4921 aaaaattact cgaccagcaa caacaactca ccctacaagc caatcaacaa atcaaaaaac
     4981 ttcacgaaca actccagcta acctatgcag aagaatcttc agaaaaagaa cccctttctg
     5041 ttactgaaga aactcaaaaa ggacaaaaca aggagaaaaa atggtggcaa ttctggcaat
     5101 aacccaacaa tttttattca taaaaattgt tgggttactt tctttttttg cttttacaag
     5161 catagcgaca tgatctcacg tcgctatttt ttaaagagca taaggaaacg cggtatcact
     5221 ttcttacgaa aggtgctagg taggctgtgc ctaccacgtt tctaagaaaa aaatttgcta
     5281 tcactttttc gtcattgtgg atagcttatg tatagtgttt cggcaaaaaa cagctataca
     5341 aatactatat ttgtatgata tacataaatt atacacaaat gcgaaaggaa ttcttctatg
     5401 gacattttag ttcggaatat tgatccaaaa gttatttcag aaatagatag acgttgccaa
     5461 gaactcacaa caaaaactgg caaaaaatgg agccgtaatg cgtacctaaa agttctaatc
     5521 gaaaacgatt ttgaccaggc acttaggcat tacaaaaaag atcaattcga tttattactc
     5581 gaaaaattta tcgatataca agcaaaaaat actgaaacat tgaacgacta tgttcataca
     5641 aacaaccaac tcattgaaac acttatcgga ggaatataac atgagaaaaa cttctgttca
     5701 aaaacacgtt accctttatc ccagtcacat tgacgtttta gattccatca tcgaaaaaaa
     5761 tccagatatc aataactac
//
