LOCUS       NZ_CP122846             5062 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC1722 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP122846
VERSION     NZ_CP122846.1
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 5062)
  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 5062)
  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
            CP122846.1.
            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..5062
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC1722"
                     /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..192
                     /locus_tag="QDX00_RS23250"
                     /old_locus_tag="QDX00_23250"
     CDS             1..192
                     /locus_tag="QDX00_RS23250"
                     /old_locus_tag="QDX00_23250"
                     /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            complement(347..565)
                     /locus_tag="QDX00_RS23255"
                     /old_locus_tag="QDX00_23255"
     CDS             complement(347..565)
                     /locus_tag="QDX00_RS23255"
                     /old_locus_tag="QDX00_23255"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001479923.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_282835968.1"
                     /translation="MFLLALSPDSVDNRITAFECADTARRSRTTERSESVSEEAEERRK
                     LHFLLTHLCGISHPAWRTFHTIRTDAT"
                     /name="hypothetical protein"
     gene            866..997
                     /locus_tag="QDX00_RS25585"
     CDS             866..997
                     /locus_tag="QDX00_RS25585"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /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_249820084.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAATGKGCTRYY"
                     /name="replication initiation protein"
     gene            1362..2420
                     /locus_tag="QDX00_RS23260"
                     /old_locus_tag="QDX00_23260"
     CDS             1362..2420
                     /locus_tag="QDX00_RS23260"
                     /old_locus_tag="QDX00_23260"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012508929.1"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="ParA family protein"
                     /protein_id="WP_094905242.1"
                     /translation="MAIYAVWNNKGGVGKSYLTFQLASEYARQNPTKKVLVIDLCPQAN
                     SSSMLLGGMVNGENTLNQIHSATQRKTISGYIEDRIRSPYIPTNTGSNYVINVSTYNSR
                     IPDNLYLVTGDEQLELQASRVVGASFPGPHDAWRTVHLWINDLISDICNSWDNGDSCVF
                     IDCNPSFSIYTELALTAAERLLIPFSADGSSKRAVKAVLSLVYGERRHLNEPQSDFYLN
                     SNRYSMSLPQIYMYVGNRLTQMNNSSASAFKTVVTEIGDEIWKVWQTKPSLFCIHPNGS
                     STPNNKKSFRNMFQYEVNDANTASVVSGALGIPIATLTAGNKNVAGRTIKVNQTQLDKQ
                     VPNIVALAGMIE"
                     /name="ParA family protein"
     gene            complement(2451..2705)
                     /locus_tag="QDX00_RS23265"
                     /old_locus_tag="QDX00_23265"
     CDS             complement(2451..2705)
                     /locus_tag="QDX00_RS23265"
                     /old_locus_tag="QDX00_23265"
                     /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_023259653.1"
                     /translation="MDSNNSQKNLQDKHADLLDKTYTLGWLDGYSEGYDDAIEDCQNAL
                     NKLENENELLNEIIENKDNVISEMASSVGRALQTVKKNK"
                     /name="hypothetical protein"
     gene            complement(2695..2880)
                     /locus_tag="QDX00_RS23270"
                     /old_locus_tag="QDX00_23270"
     CDS             complement(2695..2880)
                     /locus_tag="QDX00_RS23270"
                     /old_locus_tag="QDX00_23270"
                     /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_074518866.1"
                     /translation="MTEDNVKNISDYRKNNDAVDANSSAISGKSAPAKLSEKLRNTVPS
                     GLRAQMRQQMRNKHGF"
                     /name="hypothetical protein"
     gene            complement(3046..3207)
                     /locus_tag="QDX00_RS25590"
     CDS             complement(3046..3207)
                     /locus_tag="QDX00_RS25590"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405928.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein"
                     /protein_id="WP_074158498.1"
                     /translation="MRYPWSVSVSRKYRNARWMALRWDGETMKNGSFSVLRGGNVACTI
                     WLHRYSYG"
                     /name="mobilization protein"
     gene            complement(3238..3471)
                     /locus_tag="QDX00_RS23275"
                     /old_locus_tag="QDX00_23275"
     CDS             complement(3238..3471)
                     /locus_tag="QDX00_RS23275"
                     /old_locus_tag="QDX00_23275"
                     /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_141075289.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNEQVMQLSQQVQHLSERTERLSLLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(3478..3996)
                     /locus_tag="QDX00_RS23280"
                     /old_locus_tag="QDX00_23280"
     CDS             complement(3478..3996)
                     /locus_tag="QDX00_RS23280"
                     /old_locus_tag="QDX00_23280"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001447511.1"
                     /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_015059036.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFTTSTEESLEKHREGVKEAMMQHRKDVLKLAGNTGMRLLGIVFLLFTASG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSATVIPYQ
                     GKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            complement(<4034..4684)
                     /locus_tag="QDX00_RS23285"
                     /old_locus_tag="QDX00_23285"
                     /pseudo=""
     CDS             complement(<4034..4684)
                     /locus_tag="QDX00_RS23285"
                     /old_locus_tag="QDX00_23285"
                     /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            complement(4674..4997)
                     /locus_tag="QDX00_RS23295"
                     /old_locus_tag="QDX00_23295"
     CDS             complement(4674..4997)
                     /locus_tag="QDX00_RS23295"
                     /old_locus_tag="QDX00_23295"
                     /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_000955997.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREQRVQ
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     Typing          complement(287..368)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          392..938
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.814"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(3135..4684)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.412"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gtgactaaac aggaaaaaac cgcccttaac atggcccgct ttatcagaag ccagacatta
       61 acgctgctgg agaagctcaa cgaactggac gcggatgaac aggcagacat ctgtgaatcg
      121 cttcacgacc acgccgatga actttaccgc agttgcctcg cacgcttcgg ggatgacggt
      181 gaaaacctct gacacacaca gctcccggag acggtcacag cttgcctgtg agcggatgcc
      241 gggagcagac aagcccgtca gggcgcgtca ggccgttgac cttgcgggtg tcggggcgca
      301 gccatgaccc agtcacgtag cgatagcgga gtgtatactg gcttaactat gtggcatcag
      361 tgcggattgt atggaaagtg cgccatgccg ggtgtgaaat gccgcacaga tgcgtaagga
      421 gaaaatgcaa cttccgacgc tcttccgctt cctcgctcac tgactcgctg cgctcggtcg
      481 ttcggctgcg gcgagcggtg tctgcgcact caaaagcggt aatacggtta tccacagaat
      541 caggggataa cgccaaaaga aacatgtgag caaaaagacg aagggctaga gaaaagccgc
      601 gtagatggcg tttttccata ggctccgccc ccctgacgag catcacaaaa accgacgctc
      661 aagtcagagg tggcgaaacc cgacaggact ataaagatac caggcgtttc cccctggaag
      721 ctccctcgtg cgctctcctg ttccgaccct gccgcttacc ggatacctgt ccgcctttct
      781 cccttcggga agcgtggcgc tttctcatag ctcacgctgt tggtatctca gttcggtgta
      841 ggtcgttcgc tccaagctgg gctgtgtgca cgaacccccc gttcagcccg accgctgcgc
      901 cttatccggt aactatcgtc ttgagtccaa cccggtaaga cacgacttaa cgccactggc
      961 agcagccact ggtaagggat gtacaagata ttactaacgc agagttcttg aagttgaagc
     1021 ctaactacag ctaaactgaa aggacagatt tggtggcagt ggtcttgtac accctgttac
     1081 cacggttcag aagttcccca acttactgat ccttcgaaaa accacctccc caggtggttt
     1141 tttcgtttac agtgcagaag attacatccc acgaataagg atctcaagaa atcctttcaa
     1201 tcacgttcct actatgctga agaggtcatg ccaatacgga caccctcatc taaccatacc
     1261 gctcgaaaca cagtcagtta gctgaaagaa actaacagta gaacaataat ctctagtact
     1321 ctgacttaaa gctaacaaca aaactatatt aggagtgata gatggcgatc tatgccgtat
     1381 ggaataacaa aggcggagtg gggaaaagtt atcttacctt tcaactagcc tctgagtacg
     1441 ccagacagaa cccgacaaaa aaggttctgg tgattgatct atgcccacaa gctaactcat
     1501 cctcaatgtt acttggcggg atggttaatg gcgaaaatac gctaaatcag attcattctg
     1561 caacacaaag aaagactatt tctggatata ttgaggatag gatcagaagt ccatatattc
     1621 cgacaaatac aggttctaac tacgtaatca acgtatctac atacaatagc agaatcccag
     1681 ataatctata tcttgttact ggcgatgagc aattagaact tcaagcatca agagttgttg
     1741 gagcatcatt ccctggacct catgacgcat ggagaactgt tcatctttgg attaacgatc
     1801 taattagtga catttgtaac tcatgggata atggcgacag ctgcgttttc atcgactgta
     1861 atcccagctt ctctatttat accgagttag cattaaccgc agctgaacgc ctattaattc
     1921 cattctctgc tgatggttca tcaaaaagag ctgttaaagc agttctttct ttagtttatg
     1981 gcgagcgacg tcatctgaac gaaccacagt cagatttcta tttaaacagc aatcgttatt
     2041 ctatgtcatt accacaaata tacatgtatg ttggaaacag attaactcaa atgaacaact
     2101 catcagctag cgcattcaaa actgtggtaa cagagatcgg cgatgagatt tggaaagtgt
     2161 ggcaaacaaa accaagttta ttctgcattc atccaaatgg aagctcaacg ccgaataata
     2221 aaaaatcctt taggaacatg ttccagtatg aagtaaatga tgccaataca gcatctgtcg
     2281 tatcaggagc acttggtatt ccaattgcca cactaaccgc aggaaataag aatgttgcgg
     2341 gaagaacaat aaaggtaaat cagacacagc ttgataagca agtgcccaac attgtcgctc
     2401 ttgccggtat gattgagtaa aaaacaggcc ctttttcaag ggcctgtttt ttatttattt
     2461 ttctttaccg tttgcaacgc cctgcccaca ctagatgcca tttcactgat tacattatct
     2521 ttgttttcaa taatttcatt gagcaattcg ttttcatttt ccagtttatt caaggcattt
     2581 tgacaatctt caatggcatc atcataccct tctgaatacc catccaacca gccgagagta
     2641 taagttttat ccagaagatc agcatgctta tcttgaaggt ttttctgact gttattagaa
     2701 tccatgttta ttcctcattt gttggcgcat ttgggccctc agtccagaag gaactgtatt
     2761 tctaagtttc tcactcagct tagctggagc gcttttacct gaaatagcac tactattagc
     2821 atcaacagca tcattattct ttctgtagtc gctaatattc ttaacgttat cttcagtcat
     2881 agaacattac acctattgct gtaaacagcc caatatacgc tggagaattg aacataacac
     2941 cccttgtacg caccgctaaa atgcgttcat cgcgatcacg gcagcagaca ggtaaaaatg
     3001 gcaacaaacc acccgaaaaa ctgccgcgat cgcgcctgat aaattttaac cgtatgaata
     3061 cctatgcaac cagatggtac aggccacatt accccctctt aatacactga agctgccatt
     3121 tttcattgtt tcaccatccc agcgaagggc catccagcgt gcgttcctgt atttccggct
     3181 gacgctcacg ctccagggat aacgcatgtt cgcgctcctg tatcagccgt tcgtccctta
     3241 tctcctgttc tcgctgtata acaggctcaa gcgttctgtc cgctcgctca agtgctgcac
     3301 ctgctgactc aactgcatga cctgctcgtt cagcatcgcg ttgtcccgtt gcgtaagcga
     3361 aaacattttc tgcaattcca cgaaggcgct ctcccattcg ctcagccgct gcatatagtc
     3421 ctgttgcagt tgctctaatg cgttcagcaa atgtctttcc agctccgtca ctctgtgtca
     3481 ctccgtcagt tgtacccagt ccttcccctg atagggaatc accgttgccg atttcccgta
     3541 cggaaggacc agaaatttcc ttctcccgtc ctgcacaaac tccacgcccc atgtcttcgc
     3601 gttcagtttc tgcaatgttt cttcctgtat cctgatttct tccaggttcg cctgtatccg
     3661 cccgccaaga taccagagcg tcccgccact cgcggtaaac aggagaaaga ctatccccag
     3721 caacctcatg cccgtattcc ctgccagctt taacacgtcc ttcctgtgct gcatcatcgc
     3781 ctctttcacc ccttcccggt gtttttccag cgattcctct gtcgacgttg tgaacagggc
     3841 tatagcgtct ttgattttcg tctcgtttga ggtcacagcc ttgcttacag atttttcgag
     3901 cttgctgaac tcgtcgttca gcattgtctc tgtagattcg gctctctctt tcagcttttt
     3961 ctcgaactcc gcgcccgtct gtaaaagatt gctcataaaa tgctcctttc agcctgatat
     4021 tcttcccgcc gttcgggtct gcaatgctga tactgcttcg cgtcaccctg accacttcaa
     4081 gccctgcctc tgtgagcgcc tgaatcacat cctgacggcc ttttatctcc ccgacatgat
     4141 aaagagcgtc tatcccgcgt gtgacgctct ctgcaagcgc ctgtttcgtt tccggcagat
     4201 tatcagggag tgtcagcgtc ctgcggttct ccggggcgtt cgggtcatgc agcccgtaat
     4261 ggtgattaac cagcgtctgc caggcatcaa ttctaggcct gtctgcgcgg tcgtagtacg
     4321 gctggaggcg ttttccggtc tgtagctcca tgttcggaat gacaaaattc agctcaagcc
     4381 gtcccttgtc ctggtgctcc acccacagga tgctgtactg atttttttcg agaccgggca
     4441 tcagtacaca ctcaaagctc gccatcactt tttcacgttc tcccggcggc agctcattct
     4501 ccgcgaacga cagaacaccg gacgtgtatt tcttcgcaaa tggcgtggca tcgatgagtt
     4561 cccggacttc ttccggatta ccctgaagca ccgttgcccc ttcccggttt cgctcccttc
     4621 ccagcaggta atcaaccgga ccactgccac caccttttcc cctggcatga aacttaacta
     4681 tcatcctgca ctctctgttc cctgaccacc tgccgtaagc tgcgcaactc tctctcgatg
     4741 gccatcagtg cggccaccac ctgaacccgg tcaccggaag accactgccc gctgttcacc
     4801 ttcctcgcag tctgattcag gttattcccg atggcggcca gctgacgcag taacggcggt
     4861 gccagtgtcg gcagcttccc ggaacgggca accggctcac ccaggcagac ccgccgcatc
     4921 cataccgcca gctgtttacc ctcacagcgt tccagtaacc gtgcatgttc atcatcagta
     4981 acccgtatcg tgagcatcct ctcgcgtttc atcggtatca ttacccccat gaacagaaat
     5041 ccccccttac acggaggcat ca
//
