LOCUS       NZ_CP088190             3001 bp    DNA     circular CON 21-MAY-2024
DEFINITION  Enterococcus hirae strain S46-3 plasmid pS46-3-c, complete sequence.
ACCESSION   NZ_CP088190
VERSION     NZ_CP088190.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN23424492
            Assembly: GCF_023375175.1
KEYWORDS    RefSeq.
SOURCE      Enterococcus hirae
  ORGANISM  Enterococcus hirae
            Bacteria; Bacillota; Bacilli; Lactobacillales; Enterococcaceae;
            Enterococcus.
REFERENCE   1  (bases 1 to 3001)
  AUTHORS   Biggel,M.
  TITLE     Characteristics of florfenicol resistant enterococci from fattening
            pigs
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3001)
  AUTHORS   Biggel,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-NOV-2021) Institute for Food Safety and Hygiene,
            University of Zurich, Winterthurerstrasse 272, Zurich 8057,
            Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 140x,167x
            Sequencing Technology :: Illumina MiniSeq, Oxford Nanopore Minion
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_023375175.1-RS_2024_05_21
            Annotation Date                   :: 05/21/2024 04:03:20
            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)                     :: 2,681
            CDSs (total)                      :: 2,591
            Genes (coding)                    :: 2,499
            CDSs (with protein)               :: 2,499
            Genes (RNA)                       :: 90
            rRNAs                             :: 6, 6, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 6, 6, 6 (5S, 16S, 23S)
            tRNAs                             :: 68
            ncRNAs                            :: 4
            Pseudo Genes (total)              :: 92
            CDSs (without protein)            :: 92
            Pseudo Genes (ambiguous residues) :: 0 of 92
            Pseudo Genes (frameshifted)       :: 42 of 92
            Pseudo Genes (incomplete)         :: 38 of 92
            Pseudo Genes (internal stop)      :: 27 of 92
            Pseudo Genes (multiple problems)  :: 14 of 92
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP088190.1.
            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..3001
                     /organism="Enterococcus hirae"
                     /mol_type="genomic DNA"
                     /strain="S46-3"
                     /isolation_source="fecal sample"
                     /host="Sus scrofa domesticus"
                     /db_xref="taxon:1354"
                     /plasmid="pS46-3-c"
                     /collection_date="2021"
                     /collected_by="ILS, University of Zurich"
     gene            complement(join(2753..3001,1..489))
                     /locus_tag="LQ049_RS13340"
                     /old_locus_tag="LQ049_13345"
     CDS             complement(join(2753..3001,1..489))
                     /locus_tag="LQ049_RS13340"
                     /old_locus_tag="LQ049_13345"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002816206.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication protein"
                     /protein_id="WP_002328005.1"
                     /translation="MAVKNTKARHFGFLLYPDSIPNDWKEKLESLGISMAVSPLHDMDE
                     KKDEDTWNSNDVIRNGKHYKKPHYHVIYIARNPVTIESVRNKIKRKLGNSSIAHVEILD
                     YIKGSYEYLTHESKDAIAKNKHIYDKKNILHINDFDLDRYITLDESQKRELRDQLVEII
                     NQCGIVNLKELKAFLDWRGQEFGISNQRDVTDVIGSNGNLFRMAFDGNYQNGFRPQYAR
                     RVDPETGETISGVDELISKVKEG"
                     /name="replication protein"
     gene            complement(557..718)
                     /locus_tag="LQ049_RS13345"
                     /old_locus_tag="LQ049_13350"
     CDS             complement(557..718)
                     /locus_tag="LQ049_RS13345"
                     /old_locus_tag="LQ049_13350"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010892285.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_002328004.1"
                     /translation="MVISESKKRVMISLTKEQDRKLTDMAKQKGFSKSAVAALAIEEYA
                     RKESEQKK"
                     /name="hypothetical protein"
     gene            1480..1734
                     /locus_tag="LQ049_RS13350"
                     /old_locus_tag="LQ049_13355"
     CDS             1480..1734
                     /locus_tag="LQ049_RS13350"
                     /old_locus_tag="LQ049_13355"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_002328003.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="epsilon-antitoxin"
                     /protein_id="WP_002336587.1"
                     /translation="MTLDYRKTFEIEIINEFQSAIHSKMLNFVLNNEFDKSDSKNPQTN
                     LLNQLSNMNQINLFKLSLEELEAYHEYLRAIKKYADSIT"
                     /name="epsilon-antitoxin"
     gene            1834..2262
                     /locus_tag="LQ049_RS13355"
                     /old_locus_tag="LQ049_13360"
     CDS             1834..2262
                     /locus_tag="LQ049_RS13355"
                     /old_locus_tag="LQ049_13360"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005917942.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Hsp20/alpha crystallin family protein"
                     /protein_id="WP_202255016.1"
                     /translation="MSNEIQQRNSDTYNMTPFNFFEDFSRNLFNDFKPNLIKTDIHETD
                     NEYFVEAELPGIPKENIQVTYENGVLTISAQHQIDKETEDKKGRLLRSERSLTSVRRQY
                     LLENVKEDEIKASYSEGILKLTLPKDSNKEIKKSIPIE"
                     /name="Hsp20/alpha crystallin family protein"
ORIGIN
        1 tataatctct accaattgat ctctcagctc tcttttttga ctctcatcaa gtgttatata
       61 gcggtcaaga tcaaaatcat taatatgcaa aatatttttt ttatcgtaaa tatgtttatt
      121 cttagcaata gcatctttcg attcatgcgt aagatattca tatgaacctt tgatataatc
      181 aagtatctca acatgagcaa tcgaactatt tcccagtttt ctcttaatct tattcctaac
      241 actctctatt gttactggat ttcgagcaat atatataaca tgataatgtg gttttttata
      301 atgctttcca ttccgtataa catcattact attccacgta tcttcatctt ttttctcatc
      361 catatcgtgt aaaggactaa cagccattga aatgcctaaa ctctctaatt tttctttcca
      421 atcatttgga attgaatcag gatataataa aaacccaaaa tgtctagctt tagtattttt
      481 aacagccatg atataattac cttatcaaaa cacatgtagc gaaaactcgt atccttctaa
      541 aaacgcgaga tttcgcttat tttttttgtt ctgattcctt tcttgcatat tcttctatag
      601 ctaacgctgc aaccgcagat tttgaaaaac ctttttgttt tgccatatct gttaatttcc
      661 tatcttgctc tttagtcaga gaaatcataa ctcttttttt cgattctgaa atcaccattt
      721 aaaaaacccc tatcaaataa ttttataaaa atagtgtatc actttgtagc tatataagca
      781 acaataaaga aactaatata tagattttaa aaaaacgttg gcgaaaacgt tggcgattcg
      841 ttggcgattc aaaagtgacc aaaccccttg cccctgttag cttcaagaga ttttggcaca
      901 aaaattggca ctcggcacac tatggggggt cgtagtacgg aagcaaaatt cgcttcctcg
      961 cccccccatt ttttacaaat tccaaatttt ttccaaaaat tttccagcgc taccgctcgg
     1021 caaaattgca agcaattttt taaaccataa gaccatgagg gaatttcatt ccctcaaact
     1081 cccttgagcc tcttcctacc gaaatagtgg gctatcgctt attatttcat tcagttatcg
     1141 gctttcataa tctaacagcg aacctcttca ctgcaaagcc acgctacgct caagggcttt
     1201 tacgttacga gaaccgctgt tttaacgatt atgccgacaa ctaaacgaaa taaacgctaa
     1261 aacgccttag aacgcatttt taggctgata caggcttttt aaaaacaaaa caatagaaat
     1321 atacccataa gaatcaaaac gccttagaac gcattttata agctttaaga atgatttgct
     1381 ttttattcgc acgtttactt ttgattaaac tagcaaagtc tgtttaatta aaagtaaatg
     1441 tttagttgag caaagcgaaa ccagaaagga gcaaacacca tgacattaga ttacagaaaa
     1501 acatttgaaa tcgagataat caatgaattt caatcagcaa ttcactcaaa aatgttgaac
     1561 tttgttttaa ataatgaatt tgataaaagt gattctaaaa acccacaaac aaacttacta
     1621 aatcaattat caaacatgaa tcaaattaat ttatttaaat tatctcttga agaactagaa
     1681 gcctatcatg agtatttacg agcgataaaa aaatatgctg atagcatcac atgaaaaata
     1741 atttcacaat tttcaaatag cttaatactt gaaaactgac cttttttgac taaaataata
     1801 attgaaaaga aaatatagaa aggattgatc gttatgtcaa acgagattca acaacgtaac
     1861 tcagacacat ataacatgac accttttaat ttttttgaag actttagtcg taatttattc
     1921 aatgatttta agccaaattt aatcaaaaca gatattcatg aaactgataa tgaatatttt
     1981 gtagaagctg aacttcctgg tattcctaaa gaaaacattc aagttactta cgaaaacgga
     2041 gtattaacaa ttagtgccca acaccaaatt gataaagaaa ccgaagataa aaaaggaagg
     2101 ttgcttcgta gcgaacgtag tttaacaagt gtccgacgtc aatatttatt agaaaatgtt
     2161 aaagaagacg aaataaaagc ttcttattca gagggaattc ttaaactaac cttgccaaaa
     2221 gatagtaaca aagaaataaa aaaatctatt ccaattgagt agtaattaaa aaattacgaa
     2281 aaaaaggcgt ctataaaatt ttatagacgc ctttttttcg taaaataaat tattttttct
     2341 ttctccattc actatctaaa atcgaataaa taatttgatc ttaataacca ttatcaactt
     2401 gggtctccat tcccataatt atattaatat catttggtgt tgcagcacag aatttcagtc
     2461 tttcagtttc aaaagctata gcttgaaaca tagtaccact ccttttctat catttttata
     2521 taccaaaggg cgcacttata cgcagtaaaa aaatctaccg aattttttct acgttgtgct
     2581 aagggcgcac ttacacccac caaaatattt tggttgctat cgtgctaaaa aagagtacag
     2641 atcactcacg tgaaactgta ctctttttcc gtcaagcgtg tttgttaaaa ttcgctttgc
     2701 tcttgtctaa aattatttat caaaaaaatc tttataactc acctttattt tcttatcctt
     2761 ctttaacttt acttattagt tcgtcaacac cactgatagt ttcaccagtt tcagggtcta
     2821 ctcttcttgc atattgtggg cgaaaaccat tctggtaatt accatcaaaa gccatgcgaa
     2881 aaagattccc attcgaacca attacatcag tcacatctct ttgattagag attccaaact
     2941 cttgtcctct ccagtcaaga aaagccttta attccttcaa attgactatt ccacattgat
     3001 t
//
