LOCUS       NZ_LR135439             6299 bp    DNA     linear   CON 13-FEB-2024
DEFINITION  Enterococcus faecium isolate E8691 plasmid 5.
ACCESSION   NZ_LR135439
VERSION     NZ_LR135439.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMEA4885878
            Assembly: GCF_900639655.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus faecium
  ORGANISM  Enterococcus faecium
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 6299)
  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 03:12:57
            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)                     :: 2,795
            CDSs (total)                      :: 2,706
            Genes (coding)                    :: 2,634
            CDSs (with protein)               :: 2,634
            Genes (RNA)                       :: 89
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 67
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 72
            CDSs (without protein)            :: 72
            Pseudo Genes (ambiguous residues) :: 0 of 72
            Pseudo Genes (frameshifted)       :: 28 of 72
            Pseudo Genes (incomplete)         :: 43 of 72
            Pseudo Genes (internal stop)      :: 19 of 72
            Pseudo Genes (multiple problems)  :: 13 of 72
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            LR135439.1.
            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..6299
                     /organism="Enterococcus faecium"
                     /mol_type="genomic DNA"
                     /isolate="E8691"
                     /db_xref="taxon:1352"
                     /plasmid="5"
     gene            complement(<1..494)
                     /locus_tag="EQB50_RS14495"
     CDS             complement(<1..494)
                     /locus_tag="EQB50_RS14495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002349331.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="RNA-guided endonuclease TnpB family protein"
                     /protein_id="WP_159147954.1"
                     /translation="MEQLKAYKFRIYPTEEQEIFFAKSFGCVRKVYNLMLDDRKKAYEE
                     VKNDSSKKMTFPTPAKYKKEFPFLKEIDSLALANAQLNLDKAYKNFFRDKSVGFPRFKS
                     KKNPVQSYTTNNQNGTVALIDSKFIKVPKLKSLVRIKLHRQPKGIIKSATISRHSSGKY
                     Y"
                     /name="RNA-guided endonuclease TnpB family protein"
     gene            complement(511..915)
                     /gene="tnpA"
                     /locus_tag="EQB50_RS14500"
     CDS             complement(511..915)
                     /gene="tnpA"
                     /locus_tag="EQB50_RS14500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002287522.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS200/IS605-like element ISEfa4 family
                     transposase"
                     /protein_id="WP_002287522.1"
                     /translation="MELDTNNHSVFLLYYHLVLVTKYRRQVIDDEISDYAKTTFERISE
                     SYHITLVEWNHDKDHVHIMFKAQPKTELTKFINAYKSASSRLIKRDFPRVKQFLWKEMF
                     WSKSFCLLTTGGAPIDVIKKYIQNQGNNHK"
                     /name="tnpA"
     gene            complement(1036..1293)
                     /locus_tag="EQB50_RS14505"
     CDS             complement(1036..1293)
                     /locus_tag="EQB50_RS14505"
                     /inference="COORDINATES: protein motif:HMM:NF019884.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HTH domain-containing protein"
                     /protein_id="WP_127824027.1"
                     /translation="MTDKSIKEFAEELGVSKQAIRKYFDKLPTKLTPKLIGGKYVISAK
                     AQEFIKNSINQINEVDTEVDSLVDSILTELGRSRPSSIGG"
                     /name="HTH domain-containing protein"
     gene            complement(1303..2271)
                     /locus_tag="EQB50_RS14510"
     CDS             complement(1303..2271)
                     /locus_tag="EQB50_RS14510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002347614.1"
                     /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_002322956.1"
                     /translation="MSNEIVKYHHELNTIPLRKFTPVEMNLFFSIVSRMRDVGDKKVQF
                     TFEQLKDLSNYKATANVRFIDDLETTYDKLMDLRFGRRSADGLQRERFVLFNQFKIDGK
                     ADIPFAEIQVHEKALPLLNNLEEWVRYSLQQFNELESSYSKTMFRLLKQYRTKGFAYFS
                     KEDFHELLDIPKSYNQGTIDQRVFNPIRQELTAIFKGLTIKKKYGKGRGKPVIGYQFTF
                     KPEIKKADDFNKHAPTKEEQNRALELANRQTQHEKETTSLQERIKEQKRKLELLQQLEE
                     LEKQQKNRENETDKQKLDNNSDIPLELRKDLLDNLQNLFKD"
                     /name="replication initiation protein"
     gene            complement(2946..3074)
                     /locus_tag="EQB50_RS15085"
     CDS             complement(2946..3074)
                     /locus_tag="EQB50_RS15085"
                     /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="hypothetical protein"
                     /protein_id="WP_258079074.1"
                     /translation="MNTFSSERIRHDKAETVYFSFVMACADFFKSLGTRANIFIKL"
                     /name="hypothetical protein"
     gene            complement(3430..3594)
                     /locus_tag="EQB50_RS14755"
     CDS             complement(3430..3594)
                     /locus_tag="EQB50_RS14755"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002334262.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002334262.1"
                     /translation="MKLTKLTISLVIIAGIILYFVLPANQFFLYFGIPTILIVNGVRIF
                     EQRKKCSST"
                     /name="hypothetical protein"
     gene            complement(3613..4182)
                     /locus_tag="EQB50_RS14520"
     CDS             complement(3613..4182)
                     /locus_tag="EQB50_RS14520"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002322960.1"
                     /GO_function="GO:0004222 - metalloendopeptidase activity
                     [Evidence IEA]"
                     /GO_process="GO:0071586 - CAAX-box protein processing
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II CAAX endopeptidase family protein"
                     /protein_id="WP_002322960.1"
                     /translation="MTIKWIISIAYLVLTFAIPSLGVPSNIYFLFEHSDIFFLVLIIIL
                     FHSTFIREFKEVNLKKLFKYSFFSFSVLFLINILNTSFSEGINPNEVNGSLLLFFLNAA
                     TYGAFLEEGIFRFCMIDPQANKKQQYISILISSFLFSIVHGGGLSIFFIGIILSFVYIQ
                     TKNIWYSIVAHGFYNTIGILIYLISI"
                     /name="type II CAAX endopeptidase family protein"
     gene            complement(4182..4637)
                     /locus_tag="EQB50_RS14525"
     CDS             complement(4182..4637)
                     /locus_tag="EQB50_RS14525"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002334263.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LMxysn_1693 family intestinal colonization
                     protein"
                     /protein_id="WP_002322959.1"
                     /translation="MKKQLFKTFLLSTSILTFGSAITPSGAVFANENNISDIATYSDDE
                     YYYVLDEPVIQTRTWSKPQSWSIAKGSRTYLGIETHSRGTKLSVSANVFGMKIEIARNT
                     SASGKFKKYRQNARITVTYRVYRKVDNKYIRTQTSTANTQYIDYIPA"
                     /name="LMxysn_1693 family intestinal colonization protein"
     gene            complement(5045..5215)
                     /locus_tag="EQB50_RS14760"
     CDS             complement(5045..5215)
                     /locus_tag="EQB50_RS14760"
                     /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_002322958.1"
                     /translation="MTRKKLIFGSILLGILGFSPMLLSVINKGNKHGELKLNPNYYNSP
                     NEELFVKETDK"
                     /name="hypothetical protein"
     gene            complement(5231..>5422)
                     /locus_tag="EQB50_RS14530"
                     /pseudo=""
     CDS             complement(5231..>5422)
                     /locus_tag="EQB50_RS14530"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002292473.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="DUF536 domain-containing protein"
                     /name="DUF536 domain-containing protein"
     gene            complement(5645..>6299)
                     /locus_tag="EQB50_RS14535"
     CDS             complement(5645..>6299)
                     /locus_tag="EQB50_RS14535"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002349331.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=2
                     /transl_table=11
                     /product="RNA-guided endonuclease TnpB family protein"
                     /protein_id="WP_164851644.1"
                     /translation="SLLCKEEIIELPKTNSTIGIDLGIMDFAILSDGQKIDNNKFTSKM
                     EKKLKREQRKLSRRALLAKNKGTNLFEAKNYQKQKRKVARLHEKVMNQRTDFLNKLSTE
                     MIKNHDIICIEDLNTKGMLRNHKLAKSISDVSWSKFVTKLQYKADWYGRKIIKVDKWFP
                     SSQICSECGHKDGKKSLEIREWTCPVCHTHHDRDINASINILTEGLRLHSMGLA"
                     /name="RNA-guided endonuclease TnpB family protein"
     Typing          complement(1304..2271)
                     /name="rep_cluster_1093"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atatagtatt taccgctaga atgacgtgat attgtagcag atttgataat cccttttggt
       61 tgtctatgaa gcttaattct tactaatgac ttcaatttag gaactttgat gaatttacta
      121 tcaatcaaag caactgtacc attttgatta ttcgttgtat aactctgaac aggatttttc
      181 ttacttttga aacgtggaaa tccaacggat ttatcccgaa aaaaattctt gtatgcttta
      241 tctaaattaa gttgggcatt ggctaaagca aggctatcaa tttctttcaa aaacggaaat
      301 tctttcttgt atttagctgg tgtcggaaaa gtcatttttt tagaagaatc atttttaact
      361 tcttcatacg ccttttttcg gtcatcaagc attagattgt agaccttacg gacacaacca
      421 aaagatttgg caaagaagat ttcttgttcc tctgttggat agattctgaa tttgtatgct
      481 tttagttgtt ccataaagtt cacctacttt ctatttatga ttgtttcctt gattttggat
      541 atacttctta atcacatcaa ttggtgcgcc accagttgtc agaagacaaa agcttttaga
      601 ccagaacatt tctttccaaa gaaattgttt gactcttgga aagtcacgtt ttatcaatct
      661 tgagctggca cttttatagg cattgatgaa ttttgtcaat tctgttttag gttgagcttt
      721 gaacataata tgaacgtggt ctttatcatg attccactcc actaaagtaa tgtgatacga
      781 ttctgaaatt ctttcaaaag tagttttggc ataatcagat atttcatcat caatcacttg
      841 tctacgatat ttcgttacta aaacaaggtg gtaataaaga agaaatactg aatgattatt
      901 tgtatctaat tccatgttat atcaactcat ttcttgtata gactgattgt aacatgggac
      961 aaaataaaaa ggcaatacgc cttagttgtc ggtcttcgag ttaccaacgg taaccctcat
     1021 accgaacggc attcatcacc cacctataga ggatgggcga cttctgccta attctgttaa
     1081 aatactatca actaaactgt caacttcagt atcaacttca tttatttggt tgatactatt
     1141 ttttataaac tcttgagctt ttgctgatat tacgtatttt ccacctatca acttaggtgt
     1201 caacttggtt ggcagtttat caaaatactt tctaatggct tgtttgctga cacctagttc
     1261 ttctgcaaat tcttttattg atttatctgt catgaatact ccttagtctt taaataagtt
     1321 ttgaagatta tcaagtaagt cttttcttag ttctagagga atatcggaat tgttgtctaa
     1381 cttttgttta tccgtttcgt tttctctatt tttttgttgt ttttctaact cttctaactg
     1441 ttgtaaaagt tctaattttc gcttttgttc cttaattctt tcttgtaatg aagtagtttc
     1501 tttttcgtgt tgagtttgtc gattagctag ttctaaagcc cgattttgtt cttctttggt
     1561 tggtgcatgt ttgttaaagt cgtctgcttt tttgatttct ggtttaaatg tgaattggta
     1621 gccaatgaca ggcttcccac ggccttttcc gtatttcttt ttgattgtta aacctttaaa
     1681 gattgcggtt agttcttgtc gtattggatt gaacacacgt tgatcgatcg taccttggtt
     1741 gtaactttta ggaatatcaa gtaattcatg aaagtcttct tttgaaaaat aagcgaaacc
     1801 tttggttctg tattgtttta gtaatcgaaa cattgttttt gaataactgc tttctaattc
     1861 attgaattgt tggagagaat agcgcaccca ttcttcaaga ttattaagta agggtaaggc
     1921 tttttcatga acttgtattt cagcaaaagg aatatcagct tttccgtcga ttttaaattg
     1981 attaaataaa acaaaacgtt cacgttgcaa accgtcagca cttcttctac caaaacgtaa
     2041 atccattaat ttgtcatacg ttgtttctaa atcatctatg aatcgaacat ttgcagttgc
     2101 tttataattg cttaaatctt ttaattgctc gaatgtaaat tgtacttttt tatcacctac
     2161 atcacgcatt cttgatacga tagagaagaa caaattcatt tcgactggtg taaattttcg
     2221 caacggaatt gtatttaatt catgatgata ctttacgatt tcattagaca tatttaaaat
     2281 agctcctttc ttactcgcac aagagataca gacgttatga aatacaaaat gtctgtttat
     2341 ctacatctta tattaacatc gtcgatgtac taattcaatg tacaaacaga caaaacgatg
     2401 tagataaaca gacaaaacga tgtagataaa cagacaaaac gatgtagata aacagacaaa
     2461 acgatgtaga taaaagcgtc attcccttgg gagagtaagg atacagccga cggtaaagag
     2521 gtttaaaaag aggtttaaaa agagattata aaagaggggg acaaaatttc ccgcctaaaa
     2581 aaccacttct tttttctcca aacagattcg cgcatttttc taaactggga atcttactcc
     2641 ctatagttgc ttaaaaaggt gtgatcgctc tgctctcaca ttatactgcg cagtcgcctc
     2701 cggctccttt gctaaaactg ttcataagga actctttgag aagctatgag ccttcgtttg
     2761 agacgtttta agacagtctt agtataaatc ccttatcttg ttcttaaagc gccttacagg
     2821 cggtcagggc aagccctaac aaccctaaaa ttgtctgaat tccctctaaa attcgattta
     2881 agcactctta actctattct tatatattta tatacttaga catttgaaac gccttaaaac
     2941 gcaaattaga gcttgataaa gatatttgct cgtgtgccta gacttttaaa aaagtcggca
     3001 cacgccatga caaagctgaa ataaactgtt tcagctttgt catggcggat tcgctcactt
     3061 gaaaaagtgt tcatttcgct cgattattag catatatttt ttcgcttttt tgctagccaa
     3121 attttgcatt agttcgctca taagtcccac cctttcagta cgtccgaggg acgtatcgtt
     3181 cgtaatgtga gagtgcctat aaggtcactc tctacaaaac tcactaaaag ggtttggcaa
     3241 gctctatatt tgctagccaa atacctacgt atttggtgca aataaccgct tgtcaaaggg
     3301 gcgcaagctc ccccttgaat cccccctcaa aacccacgct ccacaataca aaaaaggcta
     3361 gcaaatgcta gccacttttt gtaaagtttc gcttgtttca ccttcggtga aattgttgct
     3421 ttgcaacgat caggtagagc tacatttttt tcgttgttca aatattctta cgccatttac
     3481 tattaaaatc gtaggtattc caaagtaaag aaaaaattga ttagcaggta atacaaaata
     3541 taaaataata ccagcaataa ttaccaaact tatagtaagt tttgttaatt tcataaagta
     3601 tgccacctta tcttatatag atatcaaata gattaatatg ccgattgtat tataaaatcc
     3661 atgagcaact atggaatacc atatattttt tgtttgtata taaacaaaac ttaaaataat
     3721 accaataaag aaaatactta ggcctccccc atgaacaata gaaaacagaa aagaagaaat
     3781 tagtattgaa atatattgtt gttttttgtt tgcttgagga tcaatcatac aaaatcgaaa
     3841 aattccttct tctaaaaaag ctccataagt agcagcattt aaaaagaata aaaggagaga
     3901 accatttact tcattaggat ttataccttc tgaaaaagat gtatttagaa tattgattag
     3961 gaataaaaca gagaatgaaa aaaaactata tttaaagagt ttttttagat ttacttcttt
     4021 gaattcacga atgaaggtag aatgaaatag tataattatt agcactaaaa aaaatatatc
     4081 actatgttca aataaaaaat atatatttga cggtactcct aatgatggga tagcaaaggt
     4141 caaaaccaag taagcaatac taattatcca ttttattgtc attaggcagg aatataatca
     4201 atatattgtg tatttgctgt agaagtttga gtacgaatat atttattatc taccttacga
     4261 taaactctgt aggttacagt tattcttgca ttttgacgat attttttaaa ttttccactt
     4321 gcagaagtgt ttctggctat ttcgattttc atcccaaata catttgcact gacagataac
     4381 tttgtacctc gactatgagt ttctatacct aaataagtac ggcttccttt agcaattgac
     4441 cagctttgag gtttagacca agtccttgtt tgaataactg gttcgtctaa cacatagtag
     4501 tactcatcat cagaataagt ggctatatca gaaatgttgt tctcattagc gaataccgct
     4561 ccgctaggag taatagcaga accaaaagtt aaaatagaag tagataataa aaaggtttta
     4621 aataactgtt ttttcatcaa aatcacctcg aatataagat acttaagaaa acgctttctt
     4681 tatataatta gaataatcag gaaatttaat gttgtcaaga gggtttattt tataaaagct
     4741 gttatattaa aggttagtag acataatgta cactatgcca agtagcccct ctaccaatgg
     4801 atagagacgc tcactttgtg atttttaatt ggtctagcta aaagcaactt tctaaagctt
     4861 gatttttcgc ggttatctat atctaattct ttgtgcattt ttatctgtca tttttttaag
     4921 acttgttatt tttgagagga tttgatacgc tttgtttgta tctcattttc atctaataaa
     4981 tggtttatgt tgctaaacta ggataatctc attttgggct gctcgttaga gcagtctttt
     5041 tttattattt atccgtttct tttacaaata actcttcgtt aggactgttg taataatttg
     5101 gattcaattt caattcacca tgtttatttc ctttattgat cactgacaat aacatcggac
     5161 tgaagcctag aattcctagt aaaatagaac caaatatgag cttttttctt gtcatgaatg
     5221 tttcctccag ttatttccat agtttccacc atttttgctt cttctttgtt tgtttttcta
     5281 tcgattctgt ttcttcagaa agagtagttg attcattttc tgaagtttct tccgtataaa
     5341 ctaattgtaa ccgtttttgt agtttgtcga tttgttgatt tgcctgcaag gtgagttgtt
     5401 gttgctggtc gagtaatttt tgttgtattt ctatgacccc ttgtaaatga tcaatttgtt
     5461 tgtttttttc ttttaattct gcaagtgaac tactcaccac ttagctaaac ctgacggttc
     5521 ttaacgcttg aagtgggagc ttcttgggaa tagagcatac ttgatagcgt atttctttac
     5581 taacagcggt gtctcttatt taccaagcta tccccgtagt tcctacggtt cttgatgatt
     5641 ggatctaagc caatcccata gaatgtagtc ttagaccttc ggtcagaata ttgatactag
     5701 cattgatatc acgatcatga tgagtatgac aaacaggaca agtccattct cgaatttcaa
     5761 gagatttctt gccatcttta tgtccgcact ctgaacaaat ctgactagac ggaaaccatt
     5821 tatctacttt gatgattttt cgtccatacc agtcagcctt gtattgtaat ttagtcacaa
     5881 actttgacca agaaacatca gaaatacttt tagctaattt atgatttcgc aacatacctt
     5941 ttgtgtttaa gtcttcaata cagataatat cgtgattttt gatcatttct gtactcaact
     6001 tattcagaaa atcagtacgt tgattcatta ctttttcatg caatctagct actttgcgtt
     6061 tttgtttttg ataattttta gcttcaaata gattggtacc tttattttta gccaataaag
     6121 cacgcctaga caatttgcgt tgttcacgct ttagtttctt ttccattttg gacgtgaatt
     6181 tattattatc aattttttgt ccatcagaaa gaatcgcaaa gtccataata cctaagtcaa
     6241 taccaattgt ggaattagtt ttaggtaatt cgataatttc ttctttacac aacaaagaa
//
