LOCUS       NZ_CP122861             5430 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC1720 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP122861
VERSION     NZ_CP122861.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32549599
            Assembly: GCF_030013865.1
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                   :: 376x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030013865.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 05:22:55
            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)                     :: 5,235
            CDSs (total)                      :: 5,114
            Genes (coding)                    :: 4,754
            CDSs (with protein)               :: 4,754
            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)              :: 360
            CDSs (without protein)            :: 360
            Pseudo Genes (ambiguous residues) :: 0 of 360
            Pseudo Genes (frameshifted)       :: 114 of 360
            Pseudo Genes (incomplete)         :: 253 of 360
            Pseudo Genes (internal stop)      :: 49 of 360
            Pseudo Genes (multiple problems)  :: 51 of 360
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122861.1.
            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="ETEC1720"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed2"
                     /geo_loc_name="Belgium"
                     /collection_date="2020"
                     /collected_by="IMM_DI04"
     gene            join(5148..5430,1..38)
                     /locus_tag="QDY31_RS23480"
                     /old_locus_tag="QDY31_23480"
     CDS             join(5148..5430,1..38)
                     /locus_tag="QDY31_RS23480"
                     /old_locus_tag="QDY31_23480"
                     /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            247..>681
                     /locus_tag="QDY31_RS23485"
                     /old_locus_tag="QDY31_23485"
                     /pseudo=""
     CDS             247..>681
                     /locus_tag="QDY31_RS23485"
                     /old_locus_tag="QDY31_23485"
                     /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            716..1201
                     /locus_tag="QDY31_RS23490"
                     /old_locus_tag="QDY31_23490"
     CDS             716..1201
                     /locus_tag="QDY31_RS23490"
                     /old_locus_tag="QDY31_23490"
                     /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            1205..1417
                     /locus_tag="QDY31_RS23495"
                     /old_locus_tag="QDY31_23495"
     CDS             1205..1417
                     /locus_tag="QDY31_RS23495"
                     /old_locus_tag="QDY31_23495"
                     /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"
     gene            2239..2649
                     /locus_tag="QDY31_RS23500"
                     /old_locus_tag="QDY31_23500"
     CDS             2239..2649
                     /locus_tag="QDY31_RS23500"
                     /old_locus_tag="QDY31_23500"
                     /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            2907..3470
                     /locus_tag="QDY31_RS23505"
                     /old_locus_tag="QDY31_23505"
     CDS             2907..3470
                     /locus_tag="QDY31_RS23505"
                     /old_locus_tag="QDY31_23505"
                     /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(3499..4125)
                     /locus_tag="QDY31_RS23510"
                     /old_locus_tag="QDY31_23510"
     CDS             complement(3499..4125)
                     /locus_tag="QDY31_RS23510"
                     /old_locus_tag="QDY31_23510"
                     /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(4427..4510)
                     /locus_tag="QDY31_RS26160"
     CDS             complement(4427..4510)
                     /locus_tag="QDY31_RS26160"
                     /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"
     Typing          4861..5040
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.339"
                     /coverage="83.0"
                     /evalue="7.539999999999999e-48"
     Typing          complement(4402..4915)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.217"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          29..1533
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.426"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          5149..5429
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.632"
                     /coverage="89.0"
                     /evalue="1.04e-51"
ORIGIN
        1 atgcggtgct ggaaaaaggg gggaatgatg atcgttaaat tccatccccg ggggcgcggt
       61 ggtggtgccg gtccggtgga ttacctgctg ggaaaagacc ggcagcgcga gggggcgacc
      121 gtgctgcagg gaaagccgga ggaagtccgg gagcttatcg atgcctcgcc gtatgcgaaa
      181 aagtacacct ccggcgtact gtcgttcgcg gaggctgagc tgccgcccgg gcagcgggag
      241 cagatcatgg ccagctttga gcgggttctg atgcccgggc tcgataaaga ccagtacagc
      301 attctgtggg tggagcacac cgacaagggg cggctggagc tgaatttcct gatccccaac
      361 acagagctgc tgaccgggaa acgcctgcag ccgtattacg atcgcgccga ccggccgcgc
      421 atcgatgcct ggcagaccgt ggtgaacggc agactggggc tgcatgatcc aaacgccccg
      481 aagaaccggc ggttactggt cacgccgtcc gcactgccgg aaacgaagct ggaagccgct
      541 caggcgatta cacggggttt gctggcctta gcctcatccg gggcgctcaa aacgcgcgag
      601 gacgtcacag ggtcgctcac tgcggcaggt tttgaggtgg tccgcaccac aaagaacagt
      661 atcagcattg ccgacccgga cggggggcga aacatccgac tgaagggagc catttatgag
      721 cagtctttta gcgctggcga aggacttgga aaagcaatcg aaagcgcagc agcagaatac
      781 ctgcgagatg ctgaaagccg cattcagcga gcacgagaag tctgtaaaag cggaactgag
      841 cgcaagcgcg aagagaatca gcgacgccat cagcgcccac gagcagggta tgaccgcggc
      901 gatgcagtcg aaccggctga gcgtgctgcg tatggttggc cggacgtggc tgaccatcac
      961 cctggtctca gtactgctga tcgccacgag cgggagcatt ctgtggtggc aggggcagca
     1021 gatcaccggg aattaccaga ctatccgggc gcaggagcgg acgcaggcca tgctgtcgga
     1081 gaagaaccac ggcgtgcagc tgtcgctctg tggggaacag aaactgtcct gcgtcaaagt
     1141 gaacccgaaa gcgggagctt acggggagga agggaactgg atggtactgg agaggaaata
     1201 gcccatgacg gaactggaaa aacagttgct gaccgcatta gagcagctac atcaggacta
     1261 ctcgcaaagg ctggacgagt gggagagcgc cttcgcggaa tggcagaaga tgtctggtct
     1321 tatgcaacgg gagaacgcgg cgctgaacga gcgcgtcacg cgcttgagtc agcaggtggc
     1381 gaacttgagc aggcagttac agcgtttgag ccagtagtgc agcggcatga aatggcggtg
     1441 gccgccgaac gggcatacga gcagcgacag catgaaaaag agctggcaga accccgtttc
     1501 cgtcagcgga gctataacgg tccgacgctg ggctgactgc gcgcatccag tgacaaaccc
     1561 caagaagaag ggctcataaa tttcccgcta aatacggtcg tgatgaaaag atcacggctc
     1621 aagagagggg gatttatgaa gatactaaaa gcgctcagtc tgatactgca atgcgtcaaa
     1681 ctggcaatgg atctgtggga gcgattcggg ggaaagtggc ctttttagtg ctttacaccg
     1741 tatttatacg cgaaaactgc tgtcattcat ctggctgcat aaccatgcag ccaggtgaaa
     1801 tttatctggc gtaaacgggg cggtttaccg ggtgctttgc taggggtttc acccgacagg
     1861 caccgtattt gcgccgaacc agcccgaagc ggtgcgggca agaactctta tgttaaattc
     1921 atctcatcgg caacctatac aggcataaaa atcagtttct ataagcggct ttcttgcacc
     1981 tacttggtga tttttttgga tgcgctgacg ttgctcgact ttaaatcacc atagaaaaat
     2041 accctttact tacataaaga tcgatctgga tgtgtatctt gacgaggttc aatacgagca
     2101 attgtttttg tatttaaggt ttcttatcgc cgttttttgc ggctctagaa aaatcaatac
     2161 aaaagatctt gaaagccacc tcgctccctg ggtacacttc cgtataagaa ctgatcgatg
     2221 tctaaaacgg attgtattat ggcttttatc tctctatcga acttggcagc gaagactgga
     2281 aggataatcc agtcgcagtg tgttacggcc acgcaaacga aaaaaagcac gggcgctgtc
     2341 gagctgggat tccgcttgag caagagcgct atggacgaga ctggtattac cattggggat
     2401 cgtgtcgaca ttctttacga caaagaagaa aaccagtgga tgattaagaa aattagtgaa
     2461 ggtggctttg gtgtgtctgg gcaaaaaaac aagcacggcg gttactcatc gtgtgctgtt
     2521 agattgacct tgcgaccagg ttttcctcgc ctttctgagg atgaagagga caacaagaag
     2581 ctactttccg atgattcatt cactcagcta agtgaaggtg taatcgtctt caggctggat
     2641 gatgaatagg aaggaccaaa aaggaaaggc agagttagtg agcgtcgcca aacaatcgac
     2701 taactccgcc ttcttgtcaa cacatcacta cctttggaag ggtggagtgt tatgggcggc
     2761 attatgttca taaacttgca ttctaataaa gaaaaaatcg tttcttttga gggatgtgaa
     2821 cacgacattt tctattctga taggtgcgat gctattggct ttggtctctt aagtttatgt
     2881 ttttaaaaac atatgaggct atacatatgc acgctttatc aatactacct tcagttgccc
     2941 gcgctaacct ggcaactaaa ttctcgtctc atttgaaggt gatcgagctc ttcaacacga
     3001 tgcaggattc ccaagttgtt gtcttgtcat cactgatcga aggccatcac ctcaccagtt
     3061 ctggtaacag tgtcaaagcc gactttgagg tcactcgctt accggcgatt atcgagatgt
     3121 tagagaaaaa atattttttc cctattcgtc atctaaatgt atctgttaaa tctgtaacta
     3181 caggaaggat gactggacaa actgtctatt tcatagagcc tgaacacatc gagcaacttc
     3241 tcgctgatcc tgagcttgtg tttgctaatc aggaaaggag cctcttcttt cgttctctcg
     3301 aaaaagaagg gaaaaatctc ggcaagctta tcgagaaaaa aggtagtgtt tctcaagccg
     3361 tcttaagcct tctacatcac gcctacaaag ataaacctct ttctgacgag atgtggaagg
     3421 agatagaaga taagttcacc catatgctgg atgaattgag cgcggcgtaa aggcaagggc
     3481 ggtcgttaga ccgccttttt agtcttctaa acctaattct ttgtgatagt ttttcagcgt
     3541 agagtaacga tagtttctga gtatgttttc atctttcttg acgttcgctt ctatgtatct
     3601 gtttacgaat ttgttgaaat cttcttgtat tttttctttg ttatcattga tatgggtaaa
     3661 ttcaggagtt ggtatcttat aggctcgcga tacatactct tctttcttaa ttagcaacgc
     3721 tttggtgtaa tccagtcctt tcttaacacc ttctgatcgc tccgaaacga atccaaattt
     3781 atggtttaaa tggcttcgta agggtatccc gaacaccaat ccgttgagat caataactac
     3841 gattccgtag cctcttactt ttccatcatt actgccgtcg agagcctctt gtaggccttt
     3901 gttatcagca taaaactggt ctgtaagggt tcttaactgt atgtaatcct gtttgctcat
     3961 ttttgatgtc cattggcatt ttcctgtaac caatgtacaa aaaaagcaaa gccctctgta
     4021 agagagggct ttgcttttct ttcgttgagt cttggatttt ttacgtgtgg cgaactctac
     4081 cgcacatctt tctttggaag cttgtttgtt taacgtgggg ctcattccta ccgccacttc
     4141 tagatttact tatatcaaaa attatatgtg aagtcaattt cgtagctgtt cttgactgga
     4201 cttactttgc cagcgtaatc ttctcctgaa acgaaaaaac caccctggca ggtggttttt
     4261 cgaaggttat ttaatcctgg cagattatct aaccgtggta acagtcttgt gcgagacgtg
     4321 tcaccaaatc cgtccttcca gtgtagcctc agtaaggcca ccacttcaag aactctcaat
     4381 acatctctcg cacatcatgt ttaccagtgg ccgttgccaa tggcgattag tcgtgtcttt
     4441 ccgggttgga ctcaagtcga tagttaccgg aaaaggcgca gcggtcggac tgaacggggg
     4501 gttcgtgcat acagtccagc ttggagcgaa ctgcctaccc ggaactgagt gtcaggcgtg
     4561 gaatgagata aacgcggcca taacagcgga atgacaccgg taaaccgaaa ggcaggaaca
     4621 ggagagcgca cgagggagcc accaggggga aacgcctggt atctttatag tcctgtcggg
     4681 tttcgccacc actgatttga gcgtcagatt tcgtgatgct tgtcaggggg gcggagccta
     4741 tggaaaaacg gcagcgccgc atccttttct tgccctgttt gtcatgccgt atgcctttgc
     4801 tcttatccgt gtgcaggtaa cgcccgccgc agccgaacgg caggagcgga agcgaccgag
     4861 tgagcgagga ggcgtaatat caccgcaacc tccatgttct cccgtacgcc ctgcagctgc
     4921 attttcccct gccacatgaa gcacttttat aaagtgttac tccgccgtaa catattaagc
     4981 cagtatacac tccgctagcg ctacgtgact ggttcagggc tgcgccccga aacccgctaa
     5041 aagccactga cgcgcctgcg gcttgtccaa caccgtgccg accgggaaac atttcccgcc
     5101 cgtcccggtg ttatcaggag gctactctgg cagacaaacg caacaagatg ctcacgatgt
     5161 gggtgacgga agacgaacac cggcggctgc tcgagcggtg cgacggcaag cagctggcgg
     5221 cgtggatgcg tcagacctgc ctcgatgaga agccggcgcg tgccggcaga ctgccgtcga
     5281 tatcgccggc gctgctgcgc cagcttgccg gtatgggtaa taacctgaac cagatcgccc
     5341 ggaaagtgaa taccggtggt gccggtcatg accgggtgca gatcgtggcc gccctgatgg
     5401 caatcgacgc gggactggag cggctgcggc
//
