LOCUS       NZ_ABQJ01000017         6258 bp    DNA     linear   CON 04-FEB-2020
DEFINITION  Enterococcus faecium E1162 Contig00017, whole genome shotgun
            sequence.
ACCESSION   NZ_ABQJ01000017
VERSION     NZ_ABQJ01000017.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN02471503
            Assembly: GCF_000172675.1
KEYWORDS    WGS; RefSeq.
SOURCE      Enterococcus faecium E1162
  ORGANISM  Enterococcus faecium E1162
            Bacteria; Firmicutes; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 6258)
  AUTHORS   van Schaik,W., Top,J., Riley,D.R., Boekhorst,J., Vrijenhoek,J.E.,
            Schapendonk,C.M., Hendrickx,A.P., Nijman,I.J., Bonten,M.J.,
            Tettelin,H. and Willems,R.J.
  TITLE     Pyrosequencing-based comparative genome analysis of the nosocomial
            pathogen Enterococcus faecium and identification of a large
            transferable pathogenicity island
  JOURNAL   BMC Genomics 11, 239 (2010)
   PUBMED   20398277
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 6258)
  AUTHORS   van Schaik,W., Top,J., Bonten,M.J.M. and Willems,R.J.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-NOV-2009) Department of Medical Microbiology,
            University Medical Center Utrecht, Heidelberglaan 100, Utrecht 3584
            CX, The Netherlands
COMMENT     ##Genome-Assembly-Data-START##
            Genome Coverage                   :: 20x
            Sequencing Technology             :: 454
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/04/2020 07:39:39
            Annotation Pipeline               :: NCBI Prokaryotic Genome
            Annotation Method                 :: Best-placed reference protein
            Annotation Software revision      :: 4.11
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA;
            Genes (total)                     :: 2,641
            CDSs (total)                      :: 2,577
            Genes (coding)                    :: 2,527
            CDSs (with protein)               :: 2,527
            Genes (RNA)                       :: 64
            rRNAs                             :: 1, 1, 1 (5S, 16S, 23S)
            complete rRNAs                    :: 1, 1, 1 (5S, 16S, 23S)
            tRNAs                             :: 57
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 50
            CDSs (without protein)            :: 50
            Pseudo Genes (ambiguous residues) :: 0 of 50
            Pseudo Genes (frameshifted)       :: 28 of 50
            Pseudo Genes (incomplete)         :: 18 of 50
            Pseudo Genes (internal stop)      :: 11 of 50
            Pseudo Genes (multiple problems)  :: 5 of 50
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence was derived from
            ABQJ01000017.
            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/
            Annotation Pipeline (PGAP)
            set; GeneMarkS-2+
            repeat_region
FEATURES             Location/Qualifiers
     source          1..6258
                     /organism="Enterococcus faecium E1162"
                     /mol_type="genomic DNA"
                     /submitter_seqid="Contig00017"
                     /strain="E1162"
                     /isolation_source="bloodstream infection of a hospitalized
                     patient"
                     /host="Homo sapiens"
                     /db_xref="taxon:535206"
                     /country="France"
                     /collection_date="1997"
     gene            complement(1..816)
                     /locus_tag="EFME1162_RS11430"
                     /old_locus_tag="EfmE1162_0366"
     CDS             complement(1..816)
                     /locus_tag="EFME1162_RS11430"
                     /old_locus_tag="EfmE1162_0366"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002376626.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="maltodextrose utilization protein MalA"
                     /protein_id="WP_002295923.1"
                     /translation="MQTFPLNYFSALRTPTQVFAGRKLLSWPKFFLIFVFLVSLMVMPV
                     TLFYANQIQAIPLEQFLSVHSLIDEQGTQKFSELELSETGLQASQQTIAVTPEILVGVS
                     LSEKQQSDHGTFIDFEKEQWVIQQKDKSGIRRYTMNYSPSFQPDSVRTPEDFQRFLERE
                     FYASNRPTIILSYSLSLGLVLFVMTSLILFGASFFLWMTRKSQLSSIHTFKESANLMLN
                     VMGIGSMAAAVVGFIHFDFILMLSVQTTITVLLLLWVFVKTRFKDKRVE"
     gene            complement(829..1680)
                     /locus_tag="EFME1162_RS11435"
                     /old_locus_tag="EfmE1162_0367"
     CDS             complement(829..1680)
                     /locus_tag="EFME1162_RS11435"
                     /old_locus_tag="EfmE1162_0367"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010750943.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="gnl|TC-DB|O06991|3.A.1.1.26"
                     /protein_id="WP_002288156.1"
                     /translation="MKKFHSSARFQKRLSHFFTYFFLLILSVIIIYPLLITASTAFKSG
                     NIAAFSLDLSSDWTLGNFTRLFSETLYGTWYKNTLIISVLTMIVQVTVVTLAGYTYSRY
                     RFIGRKSSLMFFLVIQMVPTMAALTAFYVMAFLLEALDKYWFLTMIYIGGGIPMNTWLM
                     KGYFDTVPIDLDESAKLDGAGHFRIFFQIVLPLVKPMLAVQALWAFMGPFGDFMLAKFL
                     LRTPENQTVAVGLQTFISDVTNQRVSLFAAGAILIALPICLLFFFLQKNFVTGLTSGGT
                     KG"
     gene            complement(1683..2984)
                     /locus_tag="EFME1162_RS11440"
                     /old_locus_tag="EfmE1162_0368"
     CDS             complement(1683..2984)
                     /locus_tag="EFME1162_RS11440"
                     /old_locus_tag="EfmE1162_0368"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002400236.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="gnl|TC-DB|O06990|3.A.1.1.26"
                     /protein_id="WP_002288157.1"
                     /translation="MQQDKTSNINEKKITLCSLIPGMGQFVNGQAFKGIVFFAIFVLFI
                     GQMLLGGFHALVGLVTLGSIPMEDHSLFILIEGTLQFIITIIFLIFYGLNLLDAYRVAK
                     MRQEGKKINRTMKEVIHNIGDEGFPYLLTLPAYLLMIFTIIFPVLVTLFTAFTNYDFNH
                     IPPASLIDWVGAKNFFSIFFLSSYRNTFFAVFSWTVIWTLCATTLQITLGILTAVVAHQ
                     KFIKFKRIFGIIFLLPWAVPAFITIMSFSNIFNDSVGAINTQVIPFINQLPFVDISAIS
                     WKTDPNWTKVAIILVQGWLGFPYIYVMVTGILQSISEDLYEAAKIDGANAWQRFSNITL
                     PAVFLVAAPTFITQYTGNFNNFSMIYLFNNGGPGSVGGGAGSTDILISWIYKLTTGTSP
                     QYSMASAITLIISVIVICVSLLVFKKTNAFNMGD"
     gene            complement(3131..4390)
                     /locus_tag="EFME1162_RS11445"
                     /old_locus_tag="EfmE1162_0369"
     CDS             complement(3131..4390)
                     /locus_tag="EFME1162_RS11445"
                     /old_locus_tag="EfmE1162_0369"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002346576.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="gnl|TC-DB|O06989|3.A.1.1.26"
                     /protein_id="WP_002288159.1"
                     /translation="MKKRSVKQLGLGLISLGILGGLAACGNGNSSAEGEADEGKTLTVS
                     VDSGYKDYINEIKNTFEKENDVKIKLVEKDMFDQLESLALDGPAGKGPDVMMAAYDRIG
                     ALGQQGHLAEVKLGNEAAYDETDKAQVTYDGKIYGEPAVIETLVLYYNKDLVDTAPSTF
                     KDLENLSKDSRFAFESEAGKNTGFLAKWTDFYYSYGLIAGYGGYVFGDDGTNPSDIGLN
                     NAGAVEGISYATDWFKNVWPKGMQDIKSAGDFASQQFMSNKTAAIIDGPWQAQTYKENN
                     INYGVAKIPTLNNGQPYQPFGGGKGWVVSNYAKNKDLSQKWLDYVTNQENQEKFFEMVN
                     EIPANQQARETAKAKNDELTTAVIEQYETAQAMPNIPEMGEVWTGAENLMFDAASGSKT
                     PKESADEAVKTISEAIEQKY"
     gene            complement(4492..6258)
                     /locus_tag="EFME1162_RS11450"
                     /old_locus_tag="EfmE1162_0370"
     CDS             complement(4492..6258)
                     /locus_tag="EFME1162_RS11450"
                     /old_locus_tag="EfmE1162_0370"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008271692.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="CBM34|GH13_20"
                     /protein_id="WP_002288160.1"
                     /translation="MDTAAIYHRPESEYAFLYTNTRFRIRLRTRKNDIKKVYVLCGDPY
                     TITTEKWYQKQRPMKKCLSTNVHDYWEIEVTSETRRLQYAFHVVGEDNTDCFYGDQGIF
                     PYRENVITEPNFYFRIPYFHQIDRFTIPEWVKETVWYQIFPERFANGDKANDPEHTLPW
                     GSKDPDREDFFGGDLQGVRDHLDYLTDLGVNGIYFCPIFKATSNHKYDTIDYYEVDPAF
                     GDKKLLKNLIDEAHKRGIRIMFDAVFNHMGVHSPQWQDVLKNGEKSIYKDWFHIRFFPV
                     DSYQMTDLPETAENIPYDTFAFTPFMPKLNTANPEVQKYLLDIATYWIKEFDIDGWRLD
                     VANEVDHHFWKKFREAVTEIKPDIYILGEIWHSSQAWLQGDEFHAVMNYAFTDSIKDYF
                     AKKKITASQMVSGMNHQQMLYRDQVNEGTFNLLDSHDTARILTLCQGNKELMKSVMAFM
                     FLQKGSPCIYYGTEIGMTGEDDPDCRKCMIWEKEEQDLELFGFIKELVSLRKQLSKIIS
                     EGSTQWLIVYDREDKLYFTRELEGQIIYVYFNQSKEPWVVEQENEVILSQNCQLLEDGK
                     AEIRQYGFLIMC"
ORIGIN
        1 tcattcgaca cgcttatctt tgaatcttgt tttgacaaaa acccataaaa gcagcaagac
       61 agttatcgtt gtttggacac ttagcatcaa gataaagtca aagtggataa accctacaac
      121 tgctgctgcc atggaaccta ttcccataac attcagcatc aaatttgcac tctctttgaa
      181 tgtatgaatg gatgaaagtt ggctttttct tgtcatccac aagaaaaagg aagccccgaa
      241 taaaatgaga ctcgtcatga caaataggac aagaccaaga cttaaactat aagataaaat
      301 gattgttgga cgattactgg cataaaattc tctttctaaa aatcgttgga aatcttcggg
      361 cgtacgtaca gaatctggtt ggaaagatgg gctataattc atcgtatagc ggcgtatacc
      421 agatttatcc ttttgttgga tcacccattg ttccttctca aaatcaataa aagttccatg
      481 atcggattgt tgtttctcag ataaagacac acctaccaaa atttcagggg tcacagctat
      541 cgtttgttgc gatgcttgta acccagtttc agataattca agttcagaaa atttttgggt
      601 tccttgttca tcgatcagcg aatgaacgga tagaaattgt tctaatggaa tcgcttggat
      661 ctgattggca taaaaaagag tcacaggcat gaccatcaag gaaactaaaa atacaaatat
      721 caagaaaaat ttaggccatg ataatagttt gcgtcccgca aacacttgag ttggcgtacg
      781 taatgcggaa aaatagttta acggaaatgt ttgcatgata ctctgctcct atccttttgt
      841 tccgccagat gtcaggccgg taacaaagtt cttttgtaaa aagaagaata atagacaaat
      901 cggtagtgca atcaaaattg ccccagcagc aaaaagagag actctttggt ttgtcacatc
      961 agaaataaat gtttgtaagc cgacagcaac agtctgattt tcaggtgttc gaagcaggaa
     1021 cttagctaac atgaaatccc caaaaggtcc cataaaagcc cataatgctt gaacggcgag
     1081 catcggtttg acaagcggta atacaatctg gaaaaaaatc ctgaaatgcc ctgccccatc
     1141 aagtttagca gattcatcta aatctattgg tacagtgtca aagtatcctt tcatcagcca
     1201 agtattcatt ggaattccac cgcctatata gatcattgtc aagaaccagt acttatcgag
     1261 cgcttctaat aagaaagcca tgacataaaa ggcagtcaat gctgccatag tcggtaccat
     1321 ctgaatcact aaaaagaaca tcaaacttga tttgcggccg ataaaacgat agcgactata
     1381 agtatagccc gccaaagtta ctacagtcac ttgtacgatc attgttagga cagaaatgat
     1441 caatgtattt ttataccaag tcccgtaaag tgtttcactg aatagccgag taaagtttcc
     1501 taaagtccag tcacttgaaa gatctaaact aaaagctgca atatttcctg acttgaaggc
     1561 agtacttgct gtgatcaaaa gcggatagat gataatgact gacagtatta aaagaaaaaa
     1621 gtaagtaaaa aagtgagaaa gtcgtttttg gaatcgagca ctcgaatgaa attttttcat
     1681 tgttaatccc ccatattgaa cgcatttgtc tttttaaata ccagcaatga cacacagata
     1741 acgatgacgg agataatcaa cgtgattgct gaagccatag aatactgcgg agaagttcca
     1801 gtcgtaagtt tatagatcca ggaaataaga atatcagtag aaccagctcc tccgcctacg
     1861 cttccgggac caccattgtt aaacagatag atcatggaga aattattgaa attccccgta
     1921 tactgtgtaa taaatgttgg cgctgccact aggaagacag caggaagcgt gatgtttgaa
     1981 aagcgctgcc atgcatttgc tccgtcgatt tttgctgctt catataagtc ttctgaaatc
     2041 gattgtaaga ttcctgtaac catcacatag atatagggaa atcctaacca gccctgcact
     2101 aagataattg ctactttcgt ccagttcggg tccgttttcc aagagattgc actgatatct
     2161 acaaaaggaa gctggtttat gaaaggaatc acttgagtat tgatggcacc tacgctatcg
     2221 ttgaatatat tcgaaaaact catgatagta ataaaagctg ggaccgccca tggtaataag
     2281 aaaatgatac cgaaaatacg tttgaattta ataaatttct ggtgagcaac aaccgctgtg
     2341 agaataccaa gggtgatttg caaagttgtt gcacataaag tccaaatcac ggtccacgaa
     2401 aagactgcaa aaaaagtatt acgatatgag cttaaaaaga agatactaaa aaagttttta
     2461 gcccctaccc aatcaattaa actggctggt ggaatatgat tgaagtcata attagtaaat
     2521 gcagtgaaca atgtaactag gactgggaaa atgatcgtaa aaatcatgag aagataagcg
     2581 ggaagtgtca atagataagg aaaaccttca tcacctatat tatgtatgac ttccttcatc
     2641 gtccgattga tttttttgcc ctcttgacgc atcttcgcta ctcgataagc gtctaaaaga
     2701 ttcaaaccgt aaaaaatcaa gaaaatgatt gtaatgatga attgcaaagt gccttcaatc
     2761 aaaataaata atgaatgatc ttccattggt atacttccca aagtaaccaa tcctaccaat
     2821 gcatgaaatc cgcccagaag catctgacca atgaatagga cgaatatggc gaaaaaaacg
     2881 atacctttaa aagcttggcc atttacaaac tgccccatcc ctggaataag tgaacaaagc
     2941 gtgatttttt tttcgttgat attgcttgtt ttatcttgct gcatctgaat gccccctcta
     3001 aacttgctaa accgcaaact gcttttaaga taatggcaac aagagcaaga taattttcca
     3061 tctcgctctt gccactttta tctgaagcac ctgttccatt ttttataaaa atggacggtt
     3121 atcattttaa tcagtatttt tgttctatgg cttcactgat tgtttttact gcttcatctg
     3181 cggattcttt tggtgttttt gaacctgatg ctgcatcgaa catcaagttt tctgcacctg
     3241 tccaaacttc gcccatttct gggatgtttg gcatcgcttg agctgtttca tattgttcaa
     3301 tcacagctgt tgttaattca tcgtttttag cctttgctgt ttccctagct tgttggtttg
     3361 cagggatttc atttaccatt tcaaagaatt tttcttgatt ttcctgattc gttacataat
     3421 caagccattt ttgagagagg tctttgtttt tagcataatt gctgactacc catccttttc
     3481 ctccgccaaa cggttgataa ggctgtccat tatttagagt aggaattttg gctacaccat
     3541 aattgatatt gttttctttg tatgtttgcg cttgccatgg accgtcaatg attgctgcag
     3601 ttttattgga catgaattgc tggctggcga agtctcctgc actttttatg tcttgcattc
     3661 cctttggcca aacatttttg aaccaatctg ttgcataaga gattccttct acagcacctg
     3721 cattattcaa accgatatct gaaggatttg tgccatcatc accaaataca tagccaccgt
     3781 aacctgcaat taaaccatag gaataataaa agtcagtcca tttagctaaa aatcctgtat
     3841 tttttcctgc ttctgactca aaagcaaaac gactgtcttt ggatagattc tccaaatctt
     3901 taaacgttga tggtgctgta tcgactaaat ctttgttata gtacaaaaca agggtctcga
     3961 ttactgcagg ttctccgtag atttttccat cataagtcac ttgggctttg tctgtttcat
     4021 cgtaagctgc ttcatttccc agttttactt ccgccagatg tccttgctgt cctaacgcac
     4081 cgatccggtc atatgctgcc atcataacgt caggtccctt tccagcaggc ccatctaacg
     4141 ctaatgattc caactgatcg aacatgtcct tttctactag cttgattttc acatcgtttt
     4201 ctttttcgaa agtgtttttt atttcgttta tataatcttt atatccagaa tcaacggaaa
     4261 ctgttaacgt ttttccttca tcggcttccc cttctgctga agagttacca ttgccacaag
     4321 ccgctaatcc gcctaagatt cctaaagaga ttaaccctaa acccaactgt ttcacacttc
     4381 tttttttcat cttcatttcc tcctgtgtat tcaacgtgct gttacaccct tattataatg
     4441 ggcacaaatc ttcatttgca aacgctttct tgttgttacc ggtaacagtt ttcaacacat
     4501 gatcaaaaat ccgtattgtc gtatctctgc tttcccgtct tctaacaact gacaattttg
     4561 actaagaatc acctcatttt cctgttctac tacccaaggt tcttttgact gattaaagta
     4621 aacatagatg atctgtccct ctagttcccg tgtgaaatag agcttatctt cacgatcata
     4681 tactattagc cactgagtag aaccttcaga aataatctta gacaactgtt tccttagaga
     4741 aacaagttct tttataaaac cgaatagctc tagatcttgt tcctccttct cccatatcat
     4801 acatttgcgg caatccgggt catcttcacc agtcatccct atttctgtcc cgtaatagat
     4861 acaaggagac cctttttgaa gaaacataaa ggccatcaca gacttcatca attctttgtt
     4921 accttggcaa agggtcaaga tcctggcagt atcatgagaa tctaataagt tgaatgttcc
     4981 ttcgttcacc tgatctctgt aaagcatttg ctgatgattc attccactga ccatttgtga
     5041 agctgtgatt ttcttttttg caaaataatc tttaatcgaa tctgtgaatg cataattcat
     5101 cactgcatgg aattcatccc cttgcagcca agcttgagag gaatgccaaa tctctccaag
     5161 gatatagatg tctggtttga tttctgtaac tgcttctctg aattttttcc aaaaatgatg
     5221 atcgacttca ttagcaacat caagacgcca tccatcaata tcgaattctt ttatccaata
     5281 agttgcgata tccagcaaat atttttgcac ttctggattt gctgtattta gtttcggcat
     5341 gaatggagta aaagcaaaag tatcatatgg gatattttca gcagtttctg gtaagtcagt
     5401 catctgataa gaatctactg ggaaaaaacg gatgtggaac cagtctttat agatcgattt
     5461 ttctccgttt ttgagaacgt cttgccactg tggtgaatgg acacccatat gattgaatac
     5521 agcatcgaac atgatacgta tccctctttt atgtgcttca tcaatcaagt tttttaaaag
     5581 ttttttatcg ccaaaagcgg gatccacctc ataataatca atcgtatcgt atttatgatt
     5641 ggatgtggct ttaaatatgg gacaaaaata gatgccattg acgccaaggt ccgtcaagta
     5701 atccaaatga tccctcacac cttgcaaatc tcccccgaag aagtcttctc ggtctggatc
     5761 tttacttccc caaggtaaag tgtgttcggg gtcatttgct ttgtccccgt ttgcaaatct
     5821 ttcgggaaaa atttgatacc atactgtttc ttttacccat tctggaatag tgaatcgatc
     5881 gatttgatga aaataaggta ttcgaaaata aaaatttggt tcagtaatca cattttctcg
     5941 ataaggaaaa attccttgat caccgtaaaa acagtccgtg ttatcttccc caacaacatg
     6001 gaacgcatac tgtaagcgcc ttgtttcgct cgtcacttca atttcccaat aatcatgaac
     6061 attggtactt agacattttt tcattggtcg ttgtttttga taccattttt cagttgttat
     6121 ggtatatgga tctccacaaa gcacatatac ttttttgata tcatttttcc tagtacgaag
     6181 ccgaatacga aatcttgtat tcgtatatag aaatgcatat tcactttccg gtcgatgata
     6241 aattgcagct gtatccat
//
