LOCUS       NZ_CP122850             5430 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC1722 plasmid unnamed6, complete
            sequence.
ACCESSION   NZ_CP122850
VERSION     NZ_CP122850.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32549601
            Assembly: GCF_030013825.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5430)
  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 5430)
  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                   :: 221x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030013825.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 05:11:26
            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)                     :: 5,119
            CDSs (total)                      :: 4,998
            Genes (coding)                    :: 4,671
            CDSs (with protein)               :: 4,671
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 327
            CDSs (without protein)            :: 327
            Pseudo Genes (ambiguous residues) :: 0 of 327
            Pseudo Genes (frameshifted)       :: 101 of 327
            Pseudo Genes (incomplete)         :: 229 of 327
            Pseudo Genes (internal stop)      :: 45 of 327
            Pseudo Genes (multiple problems)  :: 44 of 327
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122850.1.
            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..5430
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC1722"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed6"
                     /geo_loc_name="Belgium"
                     /collection_date="2020"
                     /collected_by="IMM_DI04"
     gene            604..1014
                     /locus_tag="QDX00_RS24885"
                     /old_locus_tag="QDX00_24885"
     CDS             604..1014
                     /locus_tag="QDX00_RS24885"
                     /old_locus_tag="QDX00_24885"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000874179.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000874179.1"
                     /translation="MAFISLSNLAAKTGRIIQSQCVTATQTKKSTGAVELGFRLSKSAM
                     DETGITIGDRVDILYDKEENQWMIKKISEGGFGVSGQKNKHGGYSSCAVRLTLRPGFPR
                     LSEDEEDNKKLLSDDSFTQLSEGVIVFRLDDE"
                     /name="hypothetical protein"
     gene            1272..1835
                     /locus_tag="QDX00_RS24890"
                     /old_locus_tag="QDX00_24890"
     CDS             1272..1835
                     /locus_tag="QDX00_RS24890"
                     /old_locus_tag="QDX00_24890"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015959180.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001749520.1"
                     /translation="MHALSILPSVARANLATKFSSHLKVIELFNTMQDSQVVVLSSLIE
                     GHHLTSSGNSVKADFEVTRLPAIIEMLEKKYFFPIRHLNVSVKSVTTGRMTGQTVYFIE
                     PEHIEQLLADPELVFANQERSLFFRSLEKEGKNLGKLIEKKGSVSQAVLSLLHHAYKDK
                     PLSDEMWKEIEDKFTHMLDELSAA"
                     /name="hypothetical protein"
     gene            complement(1864..2490)
                     /locus_tag="QDX00_RS24895"
                     /old_locus_tag="QDX00_24895"
     CDS             complement(1864..2490)
                     /locus_tag="QDX00_RS24895"
                     /old_locus_tag="QDX00_24895"
                     /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_223149424.1"
                     /translation="MSPTLNKQASKERCAVEFATRKKSKTQRKKSKALSYRGLCFFCTL
                     VTGKCQWTSKMSKQDYIQLRTLTDQFYADNKGLQEALDGSNDGKVRGYGIVVIDLNGLV
                     FGIPLRSHLNHKFGFVSERSEGVKKGLDYTKALLIKKEEYVSRAYKIPTPEFTHINDNK
                     EKIQEDFNKFVNRYIEANVKKDENILRNYRYSTLKNYHKELGLED"
                     /name="hypothetical protein"
     gene            complement(2792..2875)
                     /locus_tag="QDX00_RS25630"
     CDS             complement(2792..2875)
                     /locus_tag="QDX00_RS25630"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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_071532987.1"
                     /translation="MHEPPVQSDRCAFSGNYRLESNPERHD"
                     /name="replication initiation protein"
     gene            3513..3833
                     /locus_tag="QDX00_RS24900"
                     /old_locus_tag="QDX00_24900"
     CDS             3513..3833
                     /locus_tag="QDX00_RS24900"
                     /old_locus_tag="QDX00_24900"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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_000957082.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGRLPSI
                     SPALLRQLAGMGNNLNQIARKVNTGGAGHDRVQIVAALMAIDAGLERLRHAVLEKGGND
                     DR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            4042..>4476
                     /locus_tag="QDX00_RS24905"
                     /old_locus_tag="QDX00_24905"
                     /pseudo=""
     CDS             4042..>4476
                     /locus_tag="QDX00_RS24905"
                     /old_locus_tag="QDX00_24905"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            4511..4996
                     /locus_tag="QDX00_RS24910"
                     /old_locus_tag="QDX00_24910"
     CDS             4511..4996
                     /locus_tag="QDX00_RS24910"
                     /old_locus_tag="QDX00_24910"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001749519.1"
                     /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_001749519.1"
                     /translation="MSSLLALAKDLEKQSKAQQQNTCEMLKAAFSEHEKSVKAELSASA
                     KRISDAISAHEQGMTAAMQSNRLSVLRMVGRTWLTITLVSVLLIATSGSILWWQGQQIT
                     GNYQTIRAQERTQAMLSEKNHGVQLSLCGEQKLSCVKVNPKAGAYGEEGNWMVLERK"
                     /name="MbeB family mobilization protein"
     gene            5000..5212
                     /locus_tag="QDX00_RS24915"
                     /old_locus_tag="QDX00_24915"
     CDS             5000..5212
                     /locus_tag="QDX00_RS24915"
                     /old_locus_tag="QDX00_24915"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137423.1"
                     /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_000137423.1"
                     /translation="MTELEKQLLTALEQLHQDYSQRLDEWESAFAEWQKMSGLMQRENA
                     ALNERVTRLSQQVANLSRQLQRLSQ"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          3226..3405
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.339"
                     /coverage="83.0"
                     /evalue="7.539999999999999e-48"
     Typing          complement(2767..3280)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.217"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          3824..5328
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.426"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgaagatac taaaagcgct cagtctgata ctgcaatgcg tcaaactggc aatggatctg
       61 tgggagcgat tcgggggaaa gtggcctttt tagtgcttta caccgtattt atacgcgaaa
      121 actgctgtca ttcatctggc tgcataacca tgcagccagg tgaaatttat ctggcgtaaa
      181 cggggcggtt taccgggtgc tttgctaggg gtttcacccg acaggcaccg tatttgcgcc
      241 gaaccagccc gaagcggtgc gggcaagaac tcttatgtta aattcatctc atcggcaacc
      301 tatacaggca taaaaatcag tttctataag cggctttctt gcacctactt ggtgattttt
      361 ttggatgcgc tgacgttgct cgactttaaa tcaccataga aaaataccct ttacttacat
      421 aaagatcgat ctggatgtgt atcttgacga ggttcaatac gagcaattgt ttttgtattt
      481 aaggtttctt atcgccgttt tttgcggctc tagaaaaatc aatacaaaag atcttgaaag
      541 ccacctcgct ccctgggtac acttccgtat aagaactgat cgatgtctaa aacggattgt
      601 attatggctt ttatctctct atcgaacttg gcagcgaaga ctggaaggat aatccagtcg
      661 cagtgtgtta cggccacgca aacgaaaaaa agcacgggcg ctgtcgagct gggattccgc
      721 ttgagcaaga gcgctatgga cgagactggt attaccattg gggatcgtgt cgacattctt
      781 tacgacaaag aagaaaacca gtggatgatt aagaaaatta gtgaaggtgg ctttggtgtg
      841 tctgggcaaa aaaacaagca cggcggttac tcatcgtgtg ctgttagatt gaccttgcga
      901 ccaggttttc ctcgcctttc tgaggatgaa gaggacaaca agaagctact ttccgatgat
      961 tcattcactc agctaagtga aggtgtaatc gtcttcaggc tggatgatga ataggaagga
     1021 ccaaaaagga aaggcagagt tagtgagcgt cgccaaacaa tcgactaact ccgccttctt
     1081 gtcaacacat cactaccttt ggaagggtgg agtgttatgg gcggcattat gttcataaac
     1141 ttgcattcta ataaagaaaa aatcgtttct tttgagggat gtgaacacga cattttctat
     1201 tctgataggt gcgatgctat tggctttggt ctcttaagtt tatgttttta aaaacatatg
     1261 aggctataca tatgcacgct ttatcaatac taccttcagt tgcccgcgct aacctggcaa
     1321 ctaaattctc gtctcatttg aaggtgatcg agctcttcaa cacgatgcag gattcccaag
     1381 ttgttgtctt gtcatcactg atcgaaggcc atcacctcac cagttctggt aacagtgtca
     1441 aagccgactt tgaggtcact cgcttaccgg cgattatcga gatgttagag aaaaaatatt
     1501 ttttccctat tcgtcatcta aatgtatctg ttaaatctgt aactacagga aggatgactg
     1561 gacaaactgt ctatttcata gagcctgaac acatcgagca acttctcgct gatcctgagc
     1621 ttgtgtttgc taatcaggaa aggagcctct tctttcgttc tctcgaaaaa gaagggaaaa
     1681 atctcggcaa gcttatcgag aaaaaaggta gtgtttctca agccgtctta agccttctac
     1741 atcacgccta caaagataaa cctctttctg acgagatgtg gaaggagata gaagataagt
     1801 tcacccatat gctggatgaa ttgagcgcgg cgtaaaggca agggcggtcg ttagaccgcc
     1861 tttttagtct tctaaaccta attctttgtg atagtttttc agcgtagagt aacgatagtt
     1921 tctgagtatg ttttcatctt tcttgacgtt cgcttctatg tatctgttta cgaatttgtt
     1981 gaaatcttct tgtatttttt ctttgttatc attgatatgg gtaaattcag gagttggtat
     2041 cttataggct cgcgatacat actcttcttt cttaattagc aacgctttgg tgtaatccag
     2101 tcctttctta acaccttctg atcgctccga aacgaatcca aatttatggt ttaaatggct
     2161 tcgtaagggt atcccgaaca ccaatccgtt gagatcaata actacgattc cgtagcctct
     2221 tacttttcca tcattactgc cgtcgagagc ctcttgtagg cctttgttat cagcataaaa
     2281 ctggtctgta agggttctta actgtatgta atcctgtttg ctcatttttg atgtccattg
     2341 gcattttcct gtaaccaatg tacaaaaaaa gcaaagccct ctgtaagaga gggctttgct
     2401 tttctttcgt tgagtcttgg attttttacg tgtggcgaac tctaccgcac atctttcttt
     2461 ggaagcttgt ttgtttaacg tggggctcat tcctaccgcc acttctagat ttacttatat
     2521 caaaaattat atgtgaagtc aatttcgtag ctgttcttga ctggacttac tttgccagcg
     2581 taatcttctc ctgaaacgaa aaaaccaccc tggcaggtgg tttttcgaag gttatttaat
     2641 cctggcagat tatctaaccg tggtaacagt cttgtgcgag acgtgtcacc aaatccgtcc
     2701 ttccagtgta gcctcagtaa ggccaccact tcaagaactc tcaatacatc tctcgcacat
     2761 catgtttacc agtggccgtt gccaatggcg attagtcgtg tctttccggg ttggactcaa
     2821 gtcgatagtt accggaaaag gcgcagcggt cggactgaac ggggggttcg tgcatacagt
     2881 ccagcttgga gcgaactgcc tacccggaac tgagtgtcag gcgtggaatg agataaacgc
     2941 ggccataaca gcggaatgac accggtaaac cgaaaggcag gaacaggaga gcgcacgagg
     3001 gagccaccag ggggaaacgc ctggtatctt tatagtcctg tcgggtttcg ccaccactga
     3061 tttgagcgtc agatttcgtg atgcttgtca ggggggcgga gcctatggaa aaacggcagc
     3121 gccgcatcct tttcttgccc tgtttgtcat gccgtatgcc tttgctctta tccgtgtgca
     3181 ggtaacgccc gccgcagccg aacggcagga gcggaagcga ccgagtgagc gaggaggcgt
     3241 aatatcaccg caacctccat gttctcccgt acgccctgca gctgcatttt cccctgccac
     3301 atgaagcact tttataaagt gttactccgc cgtaacatat taagccagta tacactccgc
     3361 tagcgctacg tgactggttc agggctgcgc cccgaaaccc gctaaaagcc actgacgcgc
     3421 ctgcggcttg tccaacaccg tgccgaccgg gaaacatttc ccgcccgtcc cggtgttatc
     3481 aggaggctac tctggcagac aaacgcaaca agatgctcac gatgtgggtg acggaagacg
     3541 aacaccggcg gctgctcgag cggtgcgacg gcaagcagct ggcggcgtgg atgcgtcaga
     3601 cctgcctcga tgagaagccg gcgcgtgccg gcagactgcc gtcgatatcg ccggcgctgc
     3661 tgcgccagct tgccggtatg ggtaataacc tgaaccagat cgcccggaaa gtgaataccg
     3721 gtggtgccgg tcatgaccgg gtgcagatcg tggccgccct gatggcaatc gacgcgggac
     3781 tggagcggct gcggcatgcg gtgctggaaa aaggggggaa tgatgatcgt taaattccat
     3841 ccccgggggc gcggtggtgg tgccggtccg gtggattacc tgctgggaaa agaccggcag
     3901 cgcgaggggg cgaccgtgct gcagggaaag ccggaggaag tccgggagct tatcgatgcc
     3961 tcgccgtatg cgaaaaagta cacctccggc gtactgtcgt tcgcggaggc tgagctgccg
     4021 cccgggcagc gggagcagat catggccagc tttgagcggg ttctgatgcc cgggctcgat
     4081 aaagaccagt acagcattct gtgggtggag cacaccgaca aggggcggct ggagctgaat
     4141 ttcctgatcc ccaacacaga gctgctgacc gggaaacgcc tgcagccgta ttacgatcgc
     4201 gccgaccggc cgcgcatcga tgcctggcag accgtggtga acggcagact ggggctgcat
     4261 gatccaaacg ccccgaagaa ccggcggtta ctggtcacgc cgtccgcact gccggaaacg
     4321 aagctggaag ccgctcaggc gattacacgg ggtttgctgg ccttagcctc atccggggcg
     4381 ctcaaaacgc gcgaggacgt cacagggtcg ctcactgcgg caggttttga ggtggtccgc
     4441 accacaaaga acagtatcag cattgccgac ccggacgggg ggcgaaacat ccgactgaag
     4501 ggagccattt atgagcagtc ttttagcgct ggcgaaggac ttggaaaagc aatcgaaagc
     4561 gcagcagcag aatacctgcg agatgctgaa agccgcattc agcgagcacg agaagtctgt
     4621 aaaagcggaa ctgagcgcaa gcgcgaagag aatcagcgac gccatcagcg cccacgagca
     4681 gggtatgacc gcggcgatgc agtcgaaccg gctgagcgtg ctgcgtatgg ttggccggac
     4741 gtggctgacc atcaccctgg tctcagtact gctgatcgcc acgagcggga gcattctgtg
     4801 gtggcagggg cagcagatca ccgggaatta ccagactatc cgggcgcagg agcggacgca
     4861 ggccatgctg tcggagaaga accacggcgt gcagctgtcg ctctgtgggg aacagaaact
     4921 gtcctgcgtc aaagtgaacc cgaaagcggg agcttacggg gaggaaggga actggatggt
     4981 actggagagg aaatagccca tgacggaact ggaaaaacag ttgctgaccg cattagagca
     5041 gctacatcag gactactcgc aaaggctgga cgagtgggag agcgccttcg cggaatggca
     5101 gaagatgtct ggtcttatgc aacgggagaa cgcggcgctg aacgagcgcg tcacgcgctt
     5161 gagtcagcag gtggcgaact tgagcaggca gttacagcgt ttgagccagt agtgcagcgg
     5221 catgaaatgg cggtggccgc cgaacgggca tacgagcagc gacagcatga aaaagagctg
     5281 gcagaacccc gtttccgtca gcggagctat aacggtccga cgctgggctg actgcgcgca
     5341 tccagtgaca aaccccaaga agaagggctc ataaatttcc cgctaaatac ggtcgtgatg
     5401 aaaagatcac ggctcaagag agggggattt
//
