LOCUS       NZ_CP122908             4066 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC1706 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP122908
VERSION     NZ_CP122908.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32549588
            Assembly: GCF_030012725.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4066)
  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 4066)
  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                   :: 125x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030012725.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 06:03:10
            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)                     :: 6,261
            CDSs (total)                      :: 6,130
            Genes (coding)                    :: 5,570
            CDSs (with protein)               :: 5,570
            Genes (RNA)                       :: 131
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 97
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 560
            CDSs (without protein)            :: 560
            Pseudo Genes (ambiguous residues) :: 0 of 560
            Pseudo Genes (frameshifted)       :: 268 of 560
            Pseudo Genes (incomplete)         :: 343 of 560
            Pseudo Genes (internal stop)      :: 69 of 560
            Pseudo Genes (multiple problems)  :: 104 of 560
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122908.1.
            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..4066
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC1706"
                     /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..2154
                     /gene="mobQ"
                     /locus_tag="QDX08_RS24620"
                     /old_locus_tag="QDX08_24620"
     CDS             1..2154
                     /gene="mobQ"
                     /locus_tag="QDX08_RS24620"
                     /old_locus_tag="QDX08_24620"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001029350.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_001029350.1"
                     /translation="MAIYHLSMKIISRSNGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPEDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGESGLAALRSQL
                     LKREEELRRKELEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQHPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMEFHLKTREAPLFAVVNTPEKQPDHLFRSLGFNRTWDEW
                     RREEDARTHATERRPDRGWSQGM"
                     /name="mobQ"
     gene            complement(2396..3103)
                     /locus_tag="QDX08_RS24625"
                     /old_locus_tag="QDX08_24625"
     CDS             complement(2396..3103)
                     /locus_tag="QDX08_RS24625"
                     /old_locus_tag="QDX08_24625"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001296720.1"
                     /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_001296720.1"
                     /translation="MTSNPLIAYKSNALVEASYKLTLQEQRFLLLCISRLNSGTDVASP
                     ELQKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRA
                     QYARGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYEILQQFRSTGE
                     RIIALDDFKSSLMLDGKYKDFKTLNRDLIKPCVDELNKKSDLAVTVETIKKGRTVVALH
                     FRFKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(3634..3888)
                     /gene="mobC"
                     /locus_tag="QDX08_RS24630"
                     /old_locus_tag="QDX08_24630"
     CDS             complement(3634..3888)
                     /gene="mobC"
                     /locus_tag="QDX08_RS24630"
                     /old_locus_tag="QDX08_24630"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091749.1"
                     /translation="MSRTLEQKIAEAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     Typing          2..359
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.214"
                     /coverage="99.0"
                     /evalue="1.43e-171"
     Typing          complement(3893..4066)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.286"
                     /coverage="98.0"
                     /evalue="2.6299999999999998e-81"
     Typing          complement(2397..3103)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2..2145
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.636"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atggcgattt atcatctcag tatgaaaatc atctccagaa gcaacggcta cagcgccgtt
       61 gcttctgctg cctatcgttc tggttcacta atgcttgatg agcgtaccgg actgactcac
      121 gactacaccc gcaaaagcgg tgtggctgag gctgtgattc tgacccccgc gacagcccct
      181 gcctggtgta cgaaccgtgc cgaactctgg aatgccgttg agaaggccga acgccggaag
      241 aactcacaac ttgcgcggga aattgaactc gctatccccc gtgaactgcc gcaggatgcc
      301 gcacgggaaa ccgttctcgc ctttgtcaga gaaaactttg tcagtcaggg catgattgct
      361 gatgtggcgt tccatcacat ggataaaaca aatccccatg cgcacatcat gctgaccacg
      421 agggctgtcg gacctgctgg gttcggcgga aaggtcaggg actggaacga ccggacacat
      481 gccgagacgt ggcgtgcatc atgggctgac catgcaaaca gggcactggc gaacgccggt
      541 tatcaggaag agatagacca tcgttcatac gagcgacagg ggcttgagaa aacgcctggt
      601 attcacctcg gaaagtctgc ctgtgcgatg gaaacacgcg gtatcgaaac agaacgcggc
      661 gaacagaatc gtctgattaa caggcttaac ctggaaatac agatttcccg caccgaactc
      721 aggaacagcg ggctgacaga gcctgcccgc cgtgtggctg accttctgaa tatcgggctt
      781 cctgacaacg caacttcgta cacactacgt gacatcatcg aagcgttgcc ggaggacagt
      841 aacgcggcat ggaaactcac cagtaacgcc atgtcgatga tggcagatat gcaggcgacg
      901 cgcagacgct gggaagagct gaacaccgaa cgaaaggaag cgatgagcca tgctgccagc
      961 ctgaaaaaat catcgccgtt ttcgtccggt ttttcccgta ttcccctgat gcaatgggct
     1021 gcaccggaat accgtagtga gcagggaaaa atccagtctc tgagccagca aatggaaaaa
     1081 ttgcgacagc attaccggaa ggtggagaaa caggacattc ccgcgagtca gacggcattt
     1141 gaaaaacagt ggcagcagtg gggggaatcc ggccttgcag ctctcagatc ccagttgctt
     1201 aaacgtgaag aggaattgcg ccggaaggag ctggaggata cagaacgtag tcgcgcggag
     1261 cagctcagaa aaaatgacaa tgccgttatg gattcagggg tgctgagagc agtcgttacg
     1321 gggtatggcg aggctcccat gcctggtaac ggggaaatga cctgttacct tctgcttcac
     1381 aaccggaacg gagaatatac gctctggggg aacgagctgg agaaataccg caccaggatc
     1441 tttgagagtg ttgatttaat gcgtgacagg agtggttata tctgtgaccg aagcgaaatc
     1501 ggtcaacatc caccactgca acgtgtttat tcctctgcga cctttgagca acttctgacg
     1561 caggtttgcc agacatggcc gcaacatacc cgcaatctcc gccaaccgaa gacatggccg
     1621 gagtctttct gtcttggaga agaccgccag ccagccatgc catcactggc agcaaggaag
     1681 gtggatttta cgcagggacg tctgccaccg acgctgatgc cggtcatgag ttctgtcgac
     1741 cgggaaaccc gccagcttca gcttttgctg gtcatgggcg tggatgactc tctgggcggt
     1801 gttgtccggc ttaatggtac gctgtatccc gcgtttgccg ttccctcagc cgataacagc
     1861 cagctggtca tcagtgcact gaccgataag gggttacggt atgcagggta tggtgttgcc
     1921 gtaaatcacg atgcagacag ccacatatca cctgcgccgg aacttatgga gtttcatctg
     1981 aaaacccgtg aggcaccgct ttttgctgtc gtcaacacac cagaaaaaca gccggatcat
     2041 ctgttccgct cgctgggttt caatcgtacc tgggacgaat ggcggcgcga ggaagatgca
     2101 cgaacacacg ccaccgagag gagacctgat cgcggttggt cacagggaat gtgaacaata
     2161 ttttgttttg tttaacatcg tgttatgttc gtcgatgttc atcgacaggg atgaatgcaa
     2221 gaagcacact cacatagcgc aaacatagtt ttgtttttcc gcccccaaaa attgggggtt
     2281 ctttttttgc tgcatcagag cgtttttgac gcaacttttc acttcaatag taccttcgca
     2341 ttcctgacac aagaaaaacg cgacagtgag cgttttaggt gccttaaaat cgattctaga
     2401 tcgtcatctt gatctgtttg tcttccttga agcgaaaatg cagggctaca accgtgcgcc
     2461 cctttttgat cgtctcaacc gttacagcca ggtcgctttt tttgttcagt tcgtcaacac
     2521 agggttttat tagatccctg tttaacgttt tgaaatcttt atatttacca tcaagcatca
     2581 gtgatgattt aaaatcatcg agggcgataa tacgttcccc agtactgcgg aattgctgga
     2641 gaatttcgta tattcttatg ctgtaacttc ttgataaatt agaaatattt ttaatgacga
     2701 ctctggtgaa ttgccccttc aactgtgtca gataaggcat taccgcgtca gaaaaagtga
     2761 tttgtgcttt cccctctccc ctcgcgtact gtgcccgata ctgaatccag cggaactcct
     2821 cgcgcttctc gtcgtccttg agaatgatcg acctgtccca caaacgatcg atcgcttcct
     2881 gtagctgaac ctcggcattt ttccgcccca tatcagggaa tgaatcaaaa tattccgcag
     2941 ctgtaatggt cattgtcttt tgcaattcag gtgaagctac gtcagtaccg gagttaagtc
     3001 ggcttatgca gagcaataag aaacgctgtt cttgtaaagt tagcttgtaa ctggcctcaa
     3061 ccagcgcatt ggacttatag gctatcagag ggtttgatgt cattttaacc accaggccaa
     3121 aaatgaggtg aaataaaaac ctatcacctt tagcattggt gagcaattat attttcaccc
     3181 cccattttcc tgtgaatatt accttaaatc tcctcacctt taccttaaat tacctcaccc
     3241 aagcacctta aattatatca cctttacctt aaattccccc acctatgcac gtgtaacgca
     3301 ttgtttttaa tcaggaattt cgaccctaaa acaagtatta aaaacaagat cttaaaaaca
     3361 agatctaaaa acttaacggc gagcctgtgg ataacttggg gtgctgaaaa taaaaatcaa
     3421 ataaaaacaa tgtattgcaa aaaatcagga ttgaaaattc cgaatacacc ccctccaacc
     3481 ctgtggaaat ccagtattca tgcgggttca gcgcatatca cctgtcgaaa aaccgtgcgt
     3541 atgtgctcaa cctggcgact gattcacttc cgcttcctcg cccactcgct cgctaacgtt
     3601 cggtcgctgg gctgcggcga gcggacgata caatcactgc tctggcagcg cctccagctc
     3661 gttaatcagc ggcagtattc gcgtcacatc agcctgccgt gtcacctctg ccttcaggaa
     3721 ctggagtaac caagctcgca actgcacttc ctccggcttt ctgacctttg ccagcaatgc
     3781 tgcacccaca atgaccttct gcgctgtgtc caggctccgg ctcttcgcct tcaggcgctg
     3841 taatctggcc tcagcttcgg caatcttctg ttcgagtgtt ctgctcattt cgtgactccg
     3901 tgcgcggtga aaaatcgcat tttagcgcgt cactggtagt ttaaaaactg agctggcata
     3961 atgcacggca aatcacgaag tgcgcactta tacaatctcc actccgtttc gattgtgtgc
     4021 gccctgcggg gctgaaagaa aactgcaaaa aggcattacg gcagaa
//
