LOCUS       NZ_CP122836             3173 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC1730 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP122836
VERSION     NZ_CP122836.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32549607
            Assembly: GCF_030013755.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3173)
  AUTHORS   Vereecke,N., Van Hoorde,S., Sperling,D., Theuns,S., Devriendt,B. and
            Cox,E.
  TITLE     Virotyping and genetic antimicrobial susceptibility testing of
            porcine ETEC/STEC strains and associated plasmid types
  JOURNAL   Front Microbiol 14, 1139312 (2023)
   PUBMED   37143544
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 3173)
  AUTHORS   Vereecke,N., Van hoorde,S., Sperling,D., Theuns,S., Devriendt,B. and
            Cox,E.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-APR-2023) Department of Pathobiology, Pharmacology and
            Zoological Medicine, Universiteit Gent, Salisburylaan 133, Merelbeke
            9820, Belgium
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method :: Trycycler; minimap2; medaka v. v0.5.3; v2.20;
            v1.5.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 126x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030013755.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 05:13:14
            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)                     :: 5,443
            CDSs (total)                      :: 5,314
            Genes (coding)                    :: 5,010
            CDSs (with protein)               :: 5,010
            Genes (RNA)                       :: 129
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 97
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 304
            CDSs (without protein)            :: 304
            Pseudo Genes (ambiguous residues) :: 0 of 304
            Pseudo Genes (frameshifted)       :: 108 of 304
            Pseudo Genes (incomplete)         :: 201 of 304
            Pseudo Genes (internal stop)      :: 42 of 304
            Pseudo Genes (multiple problems)  :: 41 of 304
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122836.1.
            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..3173
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC1730"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed4"
                     /geo_loc_name="Belgium"
                     /collection_date="2020"
                     /collected_by="IMM_DI04"
     gene            1..1110
                     /gene="wzz(fepE)"
                     /locus_tag="QDY27_RS27200"
                     /old_locus_tag="QDY27_27200"
     CDS             1..1110
                     /gene="wzz(fepE)"
                     /locus_tag="QDY27_RS27200"
                     /old_locus_tag="QDY27_27200"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001421676.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0009103 - lipopolysaccharide biosynthetic
                     process [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator Wzz(fepE)"
                     /protein_id="WP_053266246.1"
                     /translation="MKISKVSDEHFSNYNMLPNGNEGIDLFGLISVLWAAKIKIVGVIL
                     FFACIGFLVSFVLPQKWTSSAVVTPAESVQWSELNKELSKLHVLGVDFDINRDNAFDLF
                     IKKFQSVNSLNEYMRSSPYVMEMIKKNNISALELHRAIVELSKNMKSVDDNTSKKNDKS
                     SLYVSWTLSFTAPTSKEAHDVLSGYINYVSSLVVRDLMEDIRNKLEVKTNVEKEILALD
                     EIKIRNQLNADIRRLNYSLEVANAAGIKKPVYSNGQIMKDDPDFPVALGSDGIATKLNI
                     KKSIKDVSELSGELRNRQYVVNQLVVAKVGDVDFMPFQYQLSPTLPVRKDGPSNAIIVI
                     LSSVIGGMLACGYILLRHAMEARKMSVIE"
                     /name="wzz(fepE)"
     gene            complement(1355..1489)
                     /locus_tag="QDY27_RS27295"
     CDS             complement(1355..1489)
                     /locus_tag="QDY27_RS27295"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005019281.1"
                     /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_071606675.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAATGKQDVREMY"
                     /name="replication initiation protein"
     gene            complement(2135..2329)
                     /locus_tag="QDY27_RS27205"
                     /old_locus_tag="QDY27_27205"
     CDS             complement(2135..2329)
                     /locus_tag="QDY27_RS27205"
                     /old_locus_tag="QDY27_27205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_001041630.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAENETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          1969..2055
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.455"
                     /coverage="100.0"
                     /evalue="1.14e-31"
     Typing          2366..2464
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          2596..2843
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.0"
                     /coverage="86.0"
                     /evalue="1.58e-110"
     Typing          complement(1418..1944)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.956"
                     /coverage="98.0"
                     /evalue="2.2599999999999997e-176"
ORIGIN
        1 atgaaaatct caaaggtatc tgacgaacat ttttctaatt acaacatgtt gccgaatggt
       61 aatgaaggaa ttgatctttt tggcttgatt agcgttttat gggcagcaaa aataaaaatt
      121 gttggggtga ttctattttt tgcttgtatt ggctttcttg tttcttttgt tttgccacaa
      181 aaatggacta gttctgctgt ggttactcct gctgagtctg ttcaatggag tgaattaaat
      241 aaggagcttt ctaagcttca tgttctggga gtggattttg atatcaatcg tgataacgca
      301 tttgatctgt ttattaagaa attccagtcc gttaattcgt tgaatgagta tatgagatca
      361 tctccttatg ttatggagat gattaaaaag aataacatta gcgctctcga actgcatcgt
      421 gcaattgttg agttgagtaa aaatatgaag tcggttgatg ataataccag taagaaaaac
      481 gacaagtcat cattgtatgt atcatggact ctgagtttta ctgctccaac aagtaaagaa
      541 gctcacgatg tgttgtctgg gtatattaat tatgtttctt cccttgttgt aagggatttg
      601 atggaagata taagaaataa actagaagtt aaaactaatg ttgaaaaaga aattcttgca
      661 ctggatgaga taaaaattag aaaccagctg aatgcagata ttcgacgcct caattattca
      721 ctggaggttg ctaatgcggc tggaataaaa aaacctgtat acagcaatgg tcagattatg
      781 aaggatgacc cagattttcc tgtggctctc ggttctgatg gtatagcaac taaattgaac
      841 atcaaaaaat caatcaagga tgtttcggaa ttgagtgggg agttgcgaaa tcgtcaatat
      901 gttgtgaatc aattggttgt ggcgaaagtg ggggatgttg attttatgcc gtttcagtat
      961 caattgagcc caacgttacc ggtcagaaag gatgggccaa gtaatgccat aattgtaatt
     1021 ctttcttctg tcattggagg gatgcttgca tgtggctata tacttttacg tcatgccatg
     1081 gaggccagaa agatgagtgt gattgagtaa aagttgtgct gatgcatcat tttataagca
     1141 acttttataa aaagttcaaa ggatcttctt gagatcattc ccttacagcc gtagtcttct
     1201 actctagaaa acgaaaaaac cacctgggga ggtggttttt cgaaggttca gtaagttggg
     1261 gaacttctga accgtggtaa cagtcttgtg cgagacatgt caccaaatct gtccttctag
     1321 tgtagcctca gtaaggctgc cacttcaaga actctcaata catctctcgc acatcctgtt
     1381 taccagtggc cgctgccaat ggcgttaagt cgtgtcttac cgggttggac tcaagacgat
     1441 agttaccgga taaggcgcag cggtcgggct gaacgggggg ttcgtgcaca cagcccagct
     1501 tggagcgaac tgcctacccg gaactgagtg tcaggcgtgg aatgagacga acgcggccat
     1561 aacagcggaa tgacaccggt aaaccgaaag gcaggaacag gagagcgcac gagggagcca
     1621 ccagggggaa acgcctggta tctttaagtc ctgtcgggtt tcgccacctc tgacttgagc
     1681 gtcgattttt gtgatgcttg tcaggggggc ggagcctatg gaaaaacgcc accggcgcgg
     1741 ccttttttcg gggcctcttt tttgctcaca tgttttttcc ggtgttatcc cctgattctg
     1801 tggataaccg tatatccgtc tttgcgtgag cagacaccgc tcgccgcagc cgaacgaccg
     1861 agcgcagcga gtcagtgagc gaggaagcgg aagagcgccg gaagctgcat tttctcctta
     1921 cgtatctgtg cagcatttca cacctcatat gtcgctgttc tctcaccatc tgctctggcg
     1981 ccgcataatt aagctagtat acactccgct atcgctacgt gactgggtca tggctgcgcc
     2041 ccgacacccg ctaaaacccc ctgacgcgcc ctgacgggct tgtctgctga cgaaaacgcc
     2101 cacgggaaag ccgtgaccgc ctccgtcagc ttcgttatgt tcctgtttca ttttcggcct
     2161 caaagcgaat ctggatgctg ttctggagtt cttctgcgag ttcgtgcagt cgttcgcaca
     2221 tggccgcctg ttcgtcggca tccagagcat ccagtttttc aagcagtgtc aggctctggc
     2281 ttttgataaa tcgcgccata ttcagcgcag tttgttgttg tttgttcacc ttccgttgtt
     2341 ctccgtcagt tccgggtgtc ggggggaccc tgagcaggtg gtaattgtaa gacgttgcgg
     2401 gcgacggtat tacaattgca catcctgtcc tgtttcttta ggacgtatca tggcacagca
     2461 tatcaactga taaataatcc ctgtgcagtg cagccgctgt tgcataaaat ttcgctctgc
     2521 gtcgagtgtt tcttaatcaa taattccgct gatactccgg aaaaacgcga gtctgttctc
     2581 atgcctgaaa tgctcacacc ccacgcaaaa caattttttg ctgatttttc tttataaata
     2641 gagagttatg acaaattagt tcttcttgct ctctttgtga tatttaaaaa agcggtgtcg
     2701 gcgcggtgtt gtagctgcgc caacaccgct ttttaggggt ggtactgact attttcataa
     2761 aaaacatcat cttatattag gagtgctgct agcggcgcgg tgtgtttttt tacaggacgc
     2821 ccctgggggc gctgctaggg gtgtctgttc agatatgtag caatgagtca gggattcacg
     2881 aactgaaaat gtccgaaaat gtgtctcatg ggcactgtat gcgccaaaac cgatcgtcat
     2941 tcactttcat gcatagctat gcagtgagct gaaagcgatc ctgacgcatt tttccggttt
     3001 accccgggga aaacatatct ttttgcggtg tttgcggctg aatcgcgttc agcgcgtttt
     3061 agcggtgcgc gtaataaaat gttatgttaa atgtctgctg aatggttttt aggttttttc
     3121 ctaacatatg atagaataaa aaaccatatg ttaatatatt gtgttttttt tca
//
