LOCUS       NZ_CP041119             2920 bp    DNA     circular CON 20-JUN-2024
DEFINITION  Escherichia coli strain ECCTRSRTH03 plasmid unnamed9, complete
            sequence.
ACCESSION   NZ_CP041119
VERSION     NZ_CP041119.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN07450616
            Assembly: GCF_002246595.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2920)
  AUTHORS   Fouts,D., Sutton,G., Nguyen,K., White,R., D'Souza,R. and
            Thamlikitkul,V.
  TITLE     Direct Submission
  JOURNAL   Submitted (13-JUN-2019) Bioinformatics, JCVI, 9605 Medical Center
            Drive, Suite 150, Rockville, MD 20850, USA
REFERENCE   2  (bases 1 to 2920)
  AUTHORS   Fouts,D., Sutton,G., Nguyen,K., White,R., D'Souza,R. and
            Thamlikitkul,V.
  TITLE     Direct Submission
  JOURNAL   Submitted (06-JUN-2019) Bioinformatics, JCVI, 9605 Medical Center
            Drive, Suite 150, Rockville, MD 20850, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 23-MAY-2019
            Assembly Method                   :: Unicycler v. v0.4.7
            Assembly Name                     :: ECCTRSRTH03
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Reference-guided Assembly         :: NA
            Genome Coverage                   :: 150.12x
            Sequencing Technology :: Illumina NextSeq 500, Oxford Nanopore
            MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_002246595.2-RS_2024_06_20
            Annotation Date                   :: 06/20/2024 03:02:23
            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)                     :: 4,934
            CDSs (total)                      :: 4,822
            Genes (coding)                    :: 4,583
            CDSs (with protein)               :: 4,583
            Genes (RNA)                       :: 112
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 78
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 239
            CDSs (without protein)            :: 239
            Pseudo Genes (ambiguous residues) :: 0 of 239
            Pseudo Genes (frameshifted)       :: 74 of 239
            Pseudo Genes (incomplete)         :: 168 of 239
            Pseudo Genes (internal stop)      :: 35 of 239
            Pseudo Genes (multiple problems)  :: 37 of 239
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP041119.1.
            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..2920
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ECCTRSRTH03"
                     /isolation_source="Rectal swab"
                     /host="Swine"
                     /db_xref="taxon:562"
                     /plasmid="unnamed9"
                     /geo_loc_name="Thailand: Nakhon Pathom"
                     /lat_lon="13.8199 N 100.0622 E"
                     /collection_date="2016-08-01"
     gene            complement(287..790)
                     /gene="ddp1"
                     /locus_tag="CI675_RS24755"
                     /old_locus_tag="CI675_0024755"
     CDS             complement(287..790)
                     /gene="ddp1"
                     /locus_tag="CI675_RS24755"
                     /old_locus_tag="CI675_0024755"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000809479.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA distortion polypeptide 1"
                     /protein_id="WP_094316182.1"
                     /translation="MKQIKFRLTDEEYNVAHVNAISNGVNSVNAFAKRKVLDVIATPSK
                     VIVSNEPSVPVKTCLYPHELELIKRNAKLHGMSVSREIAIRLRKSVLKNEVCLYPEEVQ
                     VLRKLSTTINRVGRNIHFIISGDRFCTVNDPDFRNEIKELTALCETVDKTIEQLVFSVN
                     NRFG"
                     /name="ddp1"
     gene            complement(1104..1895)
                     /locus_tag="CI675_RS24760"
                     /old_locus_tag="CI675_0024760"
     CDS             complement(1104..1895)
                     /locus_tag="CI675_RS24760"
                     /old_locus_tag="CI675_0024760"
                     /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_094316183.1"
                     /translation="MRRSNQFPPGSLNIKLKTPLTKYAIMEIMAEYLSMLELVLGVEEF
                     KLYAYLECIVNGEKQAIYHKDKNAIVSEFTLTSMEKIKNSKLDKVAYAEDLIKEGDDEK
                     IKSILNVLNMNTESCAYETFKDKLMLVPSMVVNDLIERKLHLMEIERERKINEDRERLK
                     KEREKEKGVLKIIYNNKLSEYSCSFDYFKAVYFSSVGFLVSEKQKAKYFLAEGLESLLE
                     SYIGKKVVRLSLKGEDRKVSVIEIYNENGEFLFRTKPLTRN"
                     /name="hypothetical protein"
     gene            complement(1882..2442)
                     /locus_tag="CI675_RS24765"
                     /old_locus_tag="CI675_0024765"
     CDS             complement(1882..2442)
                     /locus_tag="CI675_RS24765"
                     /old_locus_tag="CI675_0024765"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000007848.1"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_094316184.1"
                     /translation="MSYSRYKRNPFLEGMVVPVKGKQVRLSRLGGDENILVNQSTGEVQ
                     GTHVATFKRVDSEQFVKLFTANIGLTFELSSAGIKAFGVLVWSVQNSALSKDEVDLDSF
                     VLGEFLECQVSASKQPLRLSLATFKRGLNELEKAKIIAKTMRQGRYFINPNFVFNGDRI
                     AFTTVIERKNSIGKQEDTSNEAK"
                     /name="replication/maintenance protein RepL"
     Typing          2713..2920
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.301"
                     /coverage="80.0"
                     /evalue="1.14e-81"
ORIGIN
        1 cgcgccagcc tcctgcaaag cccatttgca cggtacaagc agccactcgg ttggtaggtg
       61 gtcgtagacc gtcggtgtta cagcgatggg gggtccgggg agaaccccgg acggtttccg
      121 gtagcgctca aggcgctgcc ggaaccgtgg cggctcggtc gttccgaaga acgagaataa
      181 aaatcttcgt ggtttaactc cgatgcagga tagggcaaac gccgcaaaat gctagcattt
      241 cgctcgtttg cccagtgacc tacagtcagt tcttgataat acttttttac ccaaaacgat
      301 tattaacgct aaaaactaat tgctctattg ttttgtcgac tgtttcgcat aatgctgtaa
      361 gttcctttat ctcatttctg aaatcaggat cgttaactgt gcaaaatcga tcgccgctaa
      421 ttataaaatg aatatttcgg ccaactctat taatcgtagt tgaaagcttt ctgagcacct
      481 gtacttcttc tggataaaga caaacttcgt ttttcaaaac tgatttacgt aagcgtatcg
      541 ctatttctcg gctaacactc attccgtgta atttagcatt acgctttatt aactccagtt
      601 catgtgggta taaacatgtt tttactggta cagatggttc attcgatacg ataacctttg
      661 aaggtgttgc gataacatct aaaaccttcc tctttgcaaa agcatttaca ctattaacgc
      721 catttgaaat agcattaaca tgagcaacgt tgtattcctc gtcggtcagt ctgaatttaa
      781 tttgcttcat agtacctcct aagagcctgc cgcaggcaca ggcaaaaact cagtttttgg
      841 acaatcatgg aaaatggtac tcatttgacc atgattgtct atcctgcatt gatcgcagcc
      901 tatttaagca gttttgctca aagattgtga gtaagagcat tcgcaacaaa acaatagatt
      961 ttaataagtc gatggatgaa caagtcaatt tttctttcgt actggttaat gtttttgaac
     1021 gtcaatattc cctcgttttg aaatgagtca gctatcaata ctaaagccta caaaagaaaa
     1081 atgattatac tccacagata ctcttaattt cttgtcaatg gttttgttct aaataaaaac
     1141 tcaccatttt cattatatat ttcaattaca gaaacctttc tatcttcccc tttaagagat
     1201 aatctaacta cttttttacc tatatagctt tccagaagtg actccagtcc ttccgctaaa
     1261 aaatatttag ccttttgttt ttctgaaact aaaaagccaa cactagaaaa atacaccgct
     1321 ttaaaataat caaaagaaca agaatactca gataatttat tattgtagat gatctttagc
     1381 accccctttt ccttctccct ttccttctta agtctttctc ggtcttcatt tattttacgc
     1441 tctcgctcaa tttccattaa atggagcttc ctttcaatta aatcgtttac aaccatagaa
     1501 gggactagca ttaatttatc tttaaaagtc tcatacgcac aagattcggt attcatattt
     1561 agcacgttta agattgattt tattttttca tcatcgcctt cttttattaa atcttcagca
     1621 tatgctacct tatccaattt actatttttt attttttcca ttgatgtcaa cgtgaattct
     1681 gaaacaatcg cattcttatc tttatgatat atagcctgct tttccccatt aactatgcat
     1741 tctaaataag catagagctt aaactcctct acacctaaaa ccagttccag catagacaaa
     1801 tattctgcca taatttccat tatggcatat tttgttaatg gcgtttttaa ttttatattt
     1861 aaagaaccag gtggaaattg attacttcgc ctcattgcta gtatcctctt gttttccaat
     1921 gctatttttt ctctcgataa cagttgtaaa cgcgattctg tcaccattaa aaacaaagtt
     1981 agggttaatg aaataccttc cttgtcgcat tgtttttgca attattttcg ctttttctaa
     2041 ttcattaaga cctcgcttaa atgttgcaag acttaatcgt aatggctgtt tgctagcaga
     2101 aacttggcac tcaagaaact cacccaaaac aaagctatcc aaatccactt cgtcttttga
     2161 aagtgcagag ttctgaacag accaaactaa aacaccaaag gctttaattc ctgcagaaga
     2221 tagttcaaaa gttaagccaa tatttgctgt aaaaagtttt acaaactgtt cgctatcaac
     2281 acgtttaaaa gttgctacat gggttccttg aacctctccc gttgattggt taaccagaat
     2341 gttttcatcg cctccgagac gcgaaagcct aacctgcttc cccttgacag gtacaaccat
     2401 cccttctaaa aatgggtttc ttttatagcg actgtagctc atatttcacc ataaaaatga
     2461 tacacaggag ctaatcatag atacgcggta gctcaaaaac aaggattatt ttgagcttcg
     2521 gtagcaacag ggttgagcta ccgtagtaca gatcctgaaa acacgatccc catttcatgc
     2581 gggttgcgag agatctcctt cttagttctt aacggtagtg cgtaagtgcg tatttttcca
     2641 ttggctctct tccgcttcct cgcccactcg ctcgctacgc tcggtcgcta gggctgcggc
     2701 gagcggatcc tcctctcgca tgttgtcggt tatcccgttg ttgttctttc ggggatgagt
     2761 cgccagatag cccctaaaac gctctcagaa gctctcagac gcacgaaacg gggtttagat
     2821 gcccgccagg gcatggaagg cgcgaaaaac gcttacagag ggtttcagga ggtcaggcgc
     2881 gccgataccc ctaactaggg gctttcaggt cgccaggaac
//
