LOCUS       NZ_CP122759             4609 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC1739 plasmid unnamed1, complete
            sequence.
ACCESSION   NZ_CP122759
VERSION     NZ_CP122759.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32549616
            Assembly: GCF_030013575.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4609)
  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 4609)
  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                   :: 225x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030013575.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 05:11:44
            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)                     :: 5,204
            CDSs (total)                      :: 5,086
            Genes (coding)                    :: 4,727
            CDSs (with protein)               :: 4,727
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 359
            CDSs (without protein)            :: 359
            Pseudo Genes (ambiguous residues) :: 0 of 359
            Pseudo Genes (frameshifted)       :: 124 of 359
            Pseudo Genes (incomplete)         :: 249 of 359
            Pseudo Genes (internal stop)      :: 50 of 359
            Pseudo Genes (multiple problems)  :: 58 of 359
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122759.1.
            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..4609
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC1739"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed1"
                     /geo_loc_name="Belgium"
                     /collection_date="2021"
                     /collected_by="IMM_DI04"
     gene            1..519
                     /locus_tag="QDW95_RS23420"
                     /old_locus_tag="QDW95_23420"
     CDS             1..519
                     /locus_tag="QDW95_RS23420"
                     /old_locus_tag="QDW95_23420"
                     /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="MbeB family mobilization protein"
                     /protein_id="WP_196011041.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFSTSTEESLEKHREGVKEAMMQHRKDVLKLAGNTGMRLLGIVFLLFTASG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSATVIPYQ
                     GKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            526..759
                     /locus_tag="QDW95_RS23425"
                     /old_locus_tag="QDW95_23425"
     CDS             526..759
                     /locus_tag="QDW95_RS23425"
                     /old_locus_tag="QDW95_23425"
                     /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_000137438.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWESAFVELQKMFSLTQRDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            790..>897
                     /locus_tag="QDW95_RS26010"
                     /pseudo=""
     CDS             790..>897
                     /locus_tag="QDW95_RS26010"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405928.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein"
                     /name="mobilization protein"
     gene            1123..1359
                     /locus_tag="QDW95_RS23430"
                     /old_locus_tag="QDW95_23430"
     CDS             1123..1359
                     /locus_tag="QDW95_RS23430"
                     /old_locus_tag="QDW95_23430"
                     /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_125075503.1"
                     /translation="MSIIIDREKYTALMTLIQTSQGYVGSKVQPNGYTLKCSFDTGFAC
                     CISRNTRNSNLSVHFENESTDPATHFAILSAIS"
                     /name="hypothetical protein"
     gene            complement(1480..2304)
                     /locus_tag="QDW95_RS23435"
                     /old_locus_tag="QDW95_23435"
     CDS             complement(1480..2304)
                     /locus_tag="QDW95_RS23435"
                     /old_locus_tag="QDW95_23435"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001423320.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NYN domain-containing protein"
                     /protein_id="WP_282834334.1"
                     /translation="MLVQTCGVPQAKKQPPCGVPQAKKQPSCGEPQANTPPTACRRKKT
                     ADAVFFISKMELTPLKTIVYVDGFNFYYRKLKDSNKKWLNIKAMVEKLLPDDEIIGINY
                     YTARISGRIDSDAPRRQQIYFNALKSIDNLSIHYGTFSVNESRMFLVQPLDFKHHLKNP
                     NQKIKFANVLKTEEKGSDVNLGCHLVRDGFQGKYEKAVIITNDTDLAEPMRVVKSELSL
                     YIELLSPVNKPARTLSAICDKVTLISDQSIADSQFEDVIVVGEKTVTKPAQW"
                     /name="NYN domain-containing protein"
     gene            complement(3348..3539)
                     /locus_tag="QDW95_RS23440"
                     /old_locus_tag="QDW95_23440"
     CDS             complement(3348..3539)
                     /locus_tag="QDW95_RS23440"
                     /old_locus_tag="QDW95_23440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3606..3930
                     /locus_tag="QDW95_RS23445"
                     /old_locus_tag="QDW95_23445"
                     /pseudo=""
     CDS             3606..3930
                     /locus_tag="QDW95_RS23445"
                     /old_locus_tag="QDW95_23445"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3920..4402
                     /locus_tag="QDW95_RS23450"
                     /old_locus_tag="QDW95_23450"
     CDS             3920..4402
                     /locus_tag="QDW95_RS23450"
                     /old_locus_tag="QDW95_23450"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /protein_id="WP_282869371.1"
                     /translation="MIVKFHARGKGGGSGPVDYLLGRERNREGATVLQGNPEEIRELID
                     ATPFAKKYTSGVLSFAEKELPPGGREKVMTSFERVLMPGLEKNQYSILWVEHQDKGRLE
                     LNFVIPNMELQTGKRLQPYYDRADRPRIDAWQTLVNHHYGLHDPNAPENRRTLDPS"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     Typing          3186..3270
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.674"
                     /coverage="100.0"
                     /evalue="6.569999999999999e-34"
     Typing          complement(2631..3162)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="85.895"
                     /coverage="98.0"
                     /evalue="5.0000000000000005e-158"
     Typing          4..863
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="85.714"
                     /coverage="98.0"
                     /evalue="7.22e-138"
     Typing          3577..3887
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.192"
                     /coverage="88.0"
                     /evalue="7.56e-58"
     Typing          3921..4390
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.726"
                     /coverage="98.0"
                     /evalue="5.349999999999998e-115"
ORIGIN
        1 atgagcaatc ttttacagac gggcgcggag ttcgagaaaa agctgaaaga gagagccgaa
       61 tctacagaga caatgctgaa cgacgagttc agcaagctcg aaaaatctgt aagcaaggct
      121 gtgacctcaa acgagacgaa aatcaaagac gctatagccc tgttctcaac gtcgacagag
      181 gaatcgctgg aaaaacaccg ggaaggggtg aaagaggcga tgatgcagca caggaaggac
      241 gtgttaaagc tggcagggaa tacgggcatg aggttgctgg ggatagtctt tctcctgttt
      301 accgcgagtg gcgggacgct ctggtatctt ggcgggcgga tacaggcgaa cctggaagaa
      361 atcaggatac aggaagaaac attgcagaaa ctgaacgcga agacatgggg cgtggagttt
      421 gtgcaggacg ggagaaggaa atttctggtc cttccgtacg ggaaatcggc aacggtgatt
      481 ccctatcagg ggaaggactg ggtacaactg acggagtgat acagagtgac ggagctggaa
      541 agacatttgc tgaacgcatt agagcaactg caacaggact atatgcagcg gctgaacgaa
      601 tgggagagcg ccttcgtgga attgcagaaa atgttttcgc ttacgcaacg ggacaacgcg
      661 atgctgaacg agcaggtcat gcagttgagt cagcaggtgc agcacttgag cgagcggaca
      721 gaacgcttga gccagttata cagcgagaac aggagataag ggacgaacgg ctgatacagg
      781 aacgcgaaca tgagttatcc ctggagcgtg agcaccagcc ggaaatacag gaacgcacac
      841 tggatggtcc ttcgctggga tggtgaaact atgaaaaatg gcaggttcag tggattttga
      901 cggactaatg tagtctgcac catcttgttg cataggtatt catgcggtta aaatttatca
      961 ggcgcgatcg cggcagtttt tcgggaggtt tgttgcctgt ttttccggtt tcccgtcaga
     1021 aacgcgctga gagcgtctga ggcggtgcgg gcaacgggag ttatggtaaa tagatttatt
     1081 gctgaggttt aatgcctgca gagtaatact aatggggatg tgatgagtat tattattgat
     1141 cgtgaaaaat atactgcttt gatgacgttg atccagacat ctcaaggata tgttggctca
     1201 aaagtacaac caaatggata tacattgaag tgttctttcg acactggttt tgcatgttgt
     1261 atctctagaa atactagaaa tagtaactta tctgttcatt ttgaaaatga aagtacagat
     1321 cctgcaactc actttgctat tttaagtgct attagctaat tttttatttt ctgcacatag
     1381 ctatagattt catactcttt atatttgcct gaaggtataa tgcaaaacat aaaaagcccg
     1441 ggggacgggc tttttttcaa cagaacgagt atgtagccac taccactgtg ctggttttgt
     1501 cacggttttc tcaccaacta caataacgtc ttcaaactgg ctatcagcta ttgattggtc
     1561 gcttataaga gtgaccttat cgcatattgc gctcagggtt cttgctggtt tgtttacagg
     1621 agaaagtagt tcaatataaa ggctgagctc tgatttgact actctcattg gttcagccaa
     1681 atctgtatca ttagttatta ttacagcctt ctcgtatttc ccttggaaac catctctaac
     1741 caagtggcaa cctaaattaa cgtcagaacc cttttcttct gtctttaaga cgtttgcaaa
     1801 ctttattttt tgattcgggt tttttaagtg atgtttgaaa tcaagaggct gcactaaaaa
     1861 cattctgctt tcattcaccg aaaaagtacc ataatggata cttaggttat ctatgctttt
     1921 cagtgcattg aaatatattt gttgcctacg aggtgcgtca gaatcaatcc ttcctgagat
     1981 cctagccgtg taatagttaa ttcctattat ttcatcatcc ggtagcaatt tttcgaccat
     2041 tgcttttatg ttcagccact ttttgttgga atctttcagc ttacgataat aaaagttaaa
     2101 gccatcaaca taaactattg ttttcaatgg ggttagctcc attttagata taaaaaaaac
     2161 cgcatctgcg gtttttttcc tacggcacgc cgtaggaggg gtgtttgcct gcggctcgcc
     2221 acaggagggt tgtttcttcg cctgcggcac gccacagggg ggttgtttct tcgcctgcgg
     2281 cacgccacag gtctgtacca acattattgc attttttttg tctagtgcaa atgttttata
     2341 tggtgacgaa gtaagcccta cctaaaggag aaaagatctt cttgagatcc tttttttctg
     2401 cgcgtaatct cctgctttga aaacgaaaaa accaccctgg caggtggttt ttcgaaggtt
     2461 agttaatcct ggcagattct ctaaccgcgg taacggtctt gtgcgagaca tgtcaccaaa
     2521 tctgtccttt cagtgtagcc gtagtcaggc cgccacttca agaactctcg atacatctct
     2581 cgcacatcct gtttaccagt ggccgttgcc aatggcgatt agtcgtgtct ttccgggttg
     2641 gactcaagtt gatagttacc ggataagacg cagcggtcgg actgaacggg gggttcgtgc
     2701 atacagtcca gcttggagcg aactgccttc ccggagccga gtgtcaggcg tggaatgaga
     2761 aaccgcggcc ataacagcgg aatgacaccg gtacaccgaa aggcaggaac aggagagcgc
     2821 acgagggagc ttccaggggg aaacgcctgg tatctttata gtcctgtcgg gtttcgccac
     2881 ctctgacttg agcatcaatt tttgtgatgc tcgtcagggg ggcggagcct atggaaaaac
     2941 gcctgcggcg cggccttttt ccttggttcc ttgccttttt gttcacatgt ttctttccgg
     3001 ccttatcccc tgattctgtg gataaccgca ttaccgtctt tgcgtgagct gataccgctc
     3061 gccgcagccg aacgaccgag cgtagcgagt cagtgagcga ggaagcggaa gagcgcctga
     3121 tgcggtattt tctccttacg catctgtgcg gtatttcaca ccgcatatgc tgctcttttc
     3181 ttataatccg cactgatgcc acatagttaa gccagtatac actccgctat cgctacgtga
     3241 ctggttcagg gcttcgcccc gaaaccccct gacgcgccct gacgggcttg tctgctcccg
     3301 gcatccgctc acagacaagc tgtgaacgtc tccgggagct gtatgtgtca gaggttttca
     3361 ccgtcatccc cgaagcgtgc gaggcaacta cggtaaagct catcggcgtg gtcgtgaagc
     3421 gattcacaga tgtctgcctg ttcatccgcg tccagttcgt tgagcttctc cagcagcgtt
     3481 aatgtctggc ttctgataaa gcgcgccatg ttaagggcgg ttttttcctg tttagtcatg
     3541 gtctgatgcc tccgtgtaag ggggtttctg ttcatggggt aatgataccg atgaaacgcg
     3601 agaggatgct cacaatacgg gttactgatg atgaacatgc ccggttactt gaacgctgtg
     3661 agggtaaaca actggcggta tggatgcggc gggtctgcct gggggagccg gttgcccgtt
     3721 ccgggaaact gccgacacta gcaccgccgt tactgcgtca gctggctgcc atcgggaata
     3781 acctgaatca gacagcgagg aaggtgaaca gcgggcagtg gtcttccggt gaccgggttc
     3841 aggtggtggc cgcactgatg gccatcgaga gagaattgcg ccagcttacg gcaggtggtc
     3901 agggaacagg gagtgcggga tgatagttaa gtttcatgcc aggggaaaag gtggtggcag
     3961 tggtccggtt gattacctgc tgggaaggga gcgtaaccgg gaaggggcaa cggtgcttca
     4021 gggtaatccg gaagaaatcc gggaactcat cgatgccacg ccatttgcga agaaatacac
     4081 gtcaggtgtt ctgtcgttcg cggagaagga gctgccgccg ggaggacgtg aaaaggtgat
     4141 gacgagcttt gagcgtgtac tgatgcccgg tctcgaaaag aatcagtaca gcatcctgtg
     4201 ggtggaacac caggacaagg gacggcttga gctgaatttt gtcattccga acatggagct
     4261 acagaccgga aaacgcctcc agccgtacta cgaccgggca gacaggccga gaattgatgc
     4321 ctggcagacg ctggttaatc accattacgg gctgcatgac cccaacgccc cggagaaccg
     4381 ccggacgctt gacccttcct gataacctgc cggaaacgaa acaggcgctt gcagagagcg
     4441 atcacacgcg ggatagacgc tctttatcat gtcggggaga taaaaggccg tcaggatgtg
     4501 attcaggcgc tcacagaggc agggcttgaa gtggtcaggg tgacgcgaag cagtatcagc
     4561 attgcagacc cgaacggtgg gaagaatatc aggctgaaag gagcatttt
//
