LOCUS       NZ_CP122925             4591 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC1703 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP122925
VERSION     NZ_CP122925.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32549586
            Assembly: GCF_030012745.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4591)
  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 4591)
  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                   :: 154x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030012745.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 04:58:31
            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)                     :: 5,536
            CDSs (total)                      :: 5,404
            Genes (coding)                    :: 5,072
            CDSs (with protein)               :: 5,072
            Genes (RNA)                       :: 132
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 101
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 332
            CDSs (without protein)            :: 332
            Pseudo Genes (ambiguous residues) :: 0 of 332
            Pseudo Genes (frameshifted)       :: 124 of 332
            Pseudo Genes (incomplete)         :: 213 of 332
            Pseudo Genes (internal stop)      :: 45 of 332
            Pseudo Genes (multiple problems)  :: 44 of 332
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122925.1.
            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..4591
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC1703"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed2"
                     /geo_loc_name="Belgium"
                     /collection_date="2020"
                     /collected_by="IMM_DI04"
     gene            1..840
                     /locus_tag="QDX14_RS26410"
                     /old_locus_tag="QDX14_26410"
     CDS             1..840
                     /locus_tag="QDX14_RS26410"
                     /old_locus_tag="QDX14_26410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001354646.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001354646.1"
                     /translation="MLTLFIFFVLLIAACFFCFAPPRRGYDRNEIIPYKIKLSINKYRL
                     YIYSSGKVRQYLLFLVILSLYYSIAEPFKSELIKNISYSLMAAFIFDTGLNFSKENITK
                     GVISTRWHNDLYSSFERMKAINKIYYPSNKEINTEGLSKAITSSLFNDDANSFAKRDFR
                     LMWDLSSEKYLSYKEIIIRKGDKLDAVCLRFINDDYKFLVNFNRDEEVFKYFPSIMQPS
                     LKTYRALSRLVNSIKDPSRFKFTTESLEMELLEYLELRNELFNDIEEVMGSYAQRAP"
                     /name="hypothetical protein"
     gene            complement(1528..1761)
                     /locus_tag="QDX14_RS26415"
                     /old_locus_tag="QDX14_26415"
     CDS             complement(1528..1761)
                     /locus_tag="QDX14_RS26415"
                     /old_locus_tag="QDX14_26415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137388.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHAVTQQNNA
                     ILNERVVNLSQQVQLLAGQVDRLSRLFITNNR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1768..2328)
                     /locus_tag="QDX14_RS26420"
                     /old_locus_tag="QDX14_26420"
     CDS             complement(1768..2328)
                     /locus_tag="QDX14_RS26420"
                     /old_locus_tag="QDX14_26420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_000067488.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKQQLDTLSTTVSTQLSTTEAELSRQQKNLLWQVIKGRVLFPALTA
                     LSVTGGIFLGCWGLIQWQESRIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            complement(2341..3015)
                     /locus_tag="QDX14_RS26425"
                     /old_locus_tag="QDX14_26425"
     CDS             complement(2341..3015)
                     /locus_tag="QDX14_RS26425"
                     /old_locus_tag="QDX14_26425"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_282863387.1"
                     /translation="MIVKFHARGKGGGSGPVDYLLGRERNREGATVLRGNPEEIRELID
                     ATPFSKKYTSGVLSFAEKELPPGERERVMTSFERVLMPGLEKDQYSILWVEHQDKGRLE
                     LNFVIPNMELQSGKRLQPYYDRADRPRINAWQTLVNHHYGLRDPNAPENRRTLVTPNNL
                     PKAKQEAAEAITRGLEALYRAGAIKTRQDVTEALTAAGFEVVRTTRSSISIADPEGGGI
                     SG"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(3005..3328)
                     /locus_tag="QDX14_RS26430"
                     /old_locus_tag="QDX14_26430"
     CDS             complement(3005..3328)
                     /locus_tag="QDX14_RS26430"
                     /old_locus_tag="QDX14_26430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_001677263.1"
                     /translation="MLTIRVSDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     SPPLLRHLAAIGNNLNQTARKVNSGHWSSIDRVHVVAALMAIEGELRQLRQAVREQGGR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3391..3582
                     /locus_tag="QDX14_RS26435"
                     /old_locus_tag="QDX14_26435"
     CDS             3391..3582
                     /locus_tag="QDX14_RS26435"
                     /old_locus_tag="QDX14_26435"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /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_000165986.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            4251..4400
                     /locus_tag="QDX14_RS27715"
     CDS             4251..4400
                     /locus_tag="QDX14_RS27715"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001326446.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032194431.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPERHVKTPLAAAIGNRLEELVLK
                     LCAG"
                     /name="hypothetical protein"
     Typing          complement(3671..3755)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.837"
                     /coverage="100.0"
                     /evalue="1.41e-35"
     Typing          complement(4142..4591)
                     /name="ColRNAI_rep_cluster_1857"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(1431..2368)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.681"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(2366..3015)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="86.636"
                     /coverage="99.0"
                     /evalue="1.04e-169"
ORIGIN
        1 ttgcttacac tgttcatctt ttttgtttta ttaatagctg catgtttctt ttgttttgct
       61 ccaccacgaa gaggatatga cagaaatgag atcattccat acaaaataaa actatcaata
      121 aataaatatc gcctttacat atactcatcg ggaaaggtaa gacaatacct tttattttta
      181 gttattttat cactgtacta ctccatagcg gaaccattta agtctgagtt aataaaaaac
      241 atatcatatt cactgatggc tgcatttatt tttgatacag ggcttaattt tagcaaggag
      301 aatataacta aaggagtgat ttcaacaagg tggcataatg acctatattc atcatttgag
      361 agaatgaaag caattaataa aatttactac ccatccaaca aagagataaa cacagaaggt
      421 ctatccaaag ccatcacatc atctcttttc aatgatgacg cgaactcgtt cgcaaagaga
      481 gattttcgct tgatgtggga cttatcttct gaaaaatatc tttcctataa agaaataata
      541 ataagaaaag gcgataagct tgacgctgta tgcttgagat ttataaatga tgactacaag
      601 tttttagtta atttcaacag agatgaagag gttttcaaat actttccatc tataatgcaa
      661 ccttcactca aaacatatag agcgttatca agactagtaa actcaatcaa agatccttct
      721 agatttaagt tcacgacaga gtcattagaa atggagttac tagaatactt agagttaaga
      781 aatgaattat tcaatgacat agaagaagta atgggtagct atgctcagag ggcaccatag
      841 ttcatgatag ccctcgatag tacttactta tatttttaga gaggtttaag tgtaagtaga
      901 gggagtaaca cctggttttt cagcatccac tccaatgaat gctgacaccg atacgcgata
      961 attctcttta tcgtagcaaa atcatcctcc agattgcggt tgagaatagg ttcatggtgc
     1021 gcaatacgat tgcgcagttt tctcacggga cttgttagca gtaatgcttc cccccgggga
     1081 caaacgacag agatatacaa caaaggcccg caattaaaat actccgtatt taccataacg
     1141 tcgcattgcg cgtaccgctt aaacgcgttc agcgcgatca cggcagcaga caggtaaaaa
     1201 cagcaacaaa ccacccgaaa aactgccgcg atcgcgcctg gtaaatttta acctcatgca
     1261 tagttatgcg cgaaactgaa tgacgatcag tttcgcacgt tccagccgtc gaacggggca
     1321 aaatggggag gtttggatat tgttaatgct aatgtacgta cattaacatt ggcgccatcc
     1381 gggtagggcg tgccacaaac tggctcgatt tcagggggta ccccggtcac atccccattg
     1441 acgggccacg ccagatccgc gcttcgggtt cctgctcttc atgccagcgc cgggcaagct
     1501 cctgcgcctg acgctcctgt tcatccctta tctgttgttc gtgataaata accgactcaa
     1561 gcggtcgact tgtccggcta atagctgcac ctgctgactc aagttcacga cacgctcgtt
     1621 cagtatcgcg ttgttctgtt gcgtaaccgc gtgcatcttc tgcaattctg cgaaggcgct
     1681 ctcccactcg ttcagccgcc gcatatagtc ctgttgcaaa tgctctaagg cgttcagcaa
     1741 atgcccttcc agttccgtca tactcgttta ctccctgacc agcctcacgg cgttcttgtc
     1801 gcccaccgtc caggtgtttt cccctttcac cccgtccggc agcaccagaa atttcccgtt
     1861 ctcgccattg acgaacgtca ccccccaggt ttttgcctcg agtttcgcca gcgtgttttc
     1921 ctgctctctg atggtcaaga tatttttcgc aatcctgctt tcctgccact gaatcagccc
     1981 ccagcacccc aggaaaatgc cgcccgtgac gctgagcgcg gtcagcgccg gaaacagtac
     2041 ccgccctttg atcacctgcc agagcaggtt tttctgctgc cgggacagtt cggcctctgt
     2101 ggtgctgagc tgcgtgctca cggtggtgct cagcgtatcc agttgctgtt tcacggatgt
     2161 tgtatgttcg ctgatagcgt ctctgatttt ctgcctgttt aagctcagtg ccttgtctac
     2221 agactcttct agcttcctga actcgctgtt cagcatgttc tcggtagaag cggctcgctc
     2281 tttcagtttc ttctcgaagt ccgttcccat ttgtaaaaga ttgctcatac agcgccccct
     2341 ttagcctgag attccgcccc cctccgggtc ggcaatactg atactgcttc tggttgtcct
     2401 caccacctca aaacctgccg ctgtgagcgc ctcagtgaca tcctgacgcg tttttattgc
     2461 tccggcacgg taaagcgcct caagaccccg tgtaatcgct tctgcggcct cctgtttcgc
     2521 ttttggcaga ttattcggtg tgacaagcgt ccgtctgttc tccggtgcgt tcgggtcacg
     2581 cagcccgtaa tgatgattaa ccagcgtctg ccaggcattt atcctcggcc tgtccgcacg
     2641 gtcgtagtac ggctggaggc gcttaccgct ctgtagttcc atgttcggaa tgacaaaatt
     2701 cagttcgagc cgccccttat cctggtgttc cacccagaga atgctgtact ggtctttttc
     2761 gagaccgggc ataagaacac gctcaaagct cgtcatcact ctttcgcgtt cacccggcgg
     2821 taactccttc tccgcgaacg acagaacgcc tgacgtgtat ttcttcgaaa atggcgtggc
     2881 atcaatgagt tcccggattt cttccgggtt accccggagc accgttgcgc cttcgcggtt
     2941 acgctcccgc cccagcaggt aatcgaccgg gccacttcca ccgcctttcc ccctggcatg
     3001 aaatttaact atcatcccgt cccccctgtt ccctgacagc ctgccgcaac tggcgcaatt
     3061 caccctcgat ggccatcaga gcggccacca catgaacccg gtcaatcgaa gaccagtggc
     3121 cgctgttcac cttccgggct gtctggttca gattgttccc gatggcagcc agatgccgca
     3181 gcaatggcgg cgatagtgtc ggcagttttc ctgtgcgcgc aaccggctcc cccagacaga
     3241 cccgccgcat ccattctgcc agtcgtttac cctcgcagcg ttccagtaac cgggcgtgct
     3301 cctcatcgct aacccgtatc gtgagcatct tctcgcgttt catcggtatc attcccccta
     3361 aaaaatcccc tattaaggag ccttaagacc atgaccaaac aggaaaaaac agcccttaac
     3421 atggcccgct ttatcagaag ccagacgctg accctgctgg aaaaactcaa cgagctggac
     3481 gcggacgaac aggcagacat ctgcgaatca cttcacgacc acgccgacga actctaccgt
     3541 agttgcctcg cacgcttcgg cgatgacggt gaaagcaact gaaacatgca gctcccggag
     3601 acgctcacag cttgcctgtg agcggatgcc gggagcagac aagcccgtca gggcgcgtca
     3661 gcgggtttta gcgggtgtcg gggcgaagcc ctgacccagt cacgtagcga tagcggagtg
     3721 tatactggct taactatgtg gcatcagtgc ggattataag aaaagtgcac catatgcggt
     3781 gtgaaatacc gcacagatgc gtaaggagaa aatgccgcat caggcgctct tccgcttcct
     3841 cgctcactga ctcgctacgc tcggtcgttc ggctgcggcg agcggtatca gctcactcaa
     3901 agacggtgat gcggttatcc acagaatcag gggataacgc caaaagaaac atgtgagcaa
     3961 aaggccagga acaggaagaa ggccgcgccg ctggcgtttt tccataggct ccgccccctg
     4021 acgagcatca caaaaacaga tgctcaagtc agaggtggcg aaacccgaca ggactataaa
     4081 gataccaggc gtttccccct ggaagctccc tcgtgcgctc tcctgttccg accctgccgc
     4141 ttaccggata cctgtccgcc tttctccctt cgggaagcgt ggcgctttct catagctcac
     4201 gctgttggta tctcggcccg gtgtaggtcg ttcgctccaa gctgggctgt gtgcacgaac
     4261 cccccgttca gcccgaccgc tgcgccttat ccggtaacta tcgtcttgag tccaacccgg
     4321 aaagacacgt aaaaacgcca ctggcagcag ccattggtaa ccgtttagag gagttagtct
     4381 tgaagttatg cgccggttaa ggctaaactg aaaggacaga tttggtggct gtgctcctcc
     4441 aagccagtta ccttggttca aagagttgct gctctgagaa ccttcgaaaa gccgccttgc
     4501 tgggcggttt tttcgtttac ggacaagact accttcagga tcgttagatc tcaagacaat
     4561 catgcatagt gagcatacac aggagccgaa c
//
