LOCUS       NZ_CP122773             5880 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC1738 plasmid unnamed5, complete
            sequence.
ACCESSION   NZ_CP122773
VERSION     NZ_CP122773.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32549615
            Assembly: GCF_030013595.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5880)
  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 5880)
  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                   :: 354x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030013595.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 05:31:41
            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)                     :: 6,073
            CDSs (total)                      :: 5,947
            Genes (coding)                    :: 5,673
            CDSs (with protein)               :: 5,673
            Genes (RNA)                       :: 126
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 94
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 274
            CDSs (without protein)            :: 274
            Pseudo Genes (ambiguous residues) :: 0 of 274
            Pseudo Genes (frameshifted)       :: 109 of 274
            Pseudo Genes (incomplete)         :: 153 of 274
            Pseudo Genes (internal stop)      :: 54 of 274
            Pseudo Genes (multiple problems)  :: 34 of 274
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122773.1.
            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..5880
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC1738"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed5"
                     /geo_loc_name="Belgium"
                     /collection_date="2021"
                     /collected_by="IMM_DI04"
     gene            join(5568..5880,1..11)
                     /locus_tag="QDY55_RS30245"
                     /old_locus_tag="QDY55_30240"
     CDS             join(5568..5880,1..11)
                     /locus_tag="QDY55_RS30245"
                     /old_locus_tag="QDY55_30240"
                     /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_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            220..>651
                     /locus_tag="QDY55_RS30250"
                     /old_locus_tag="QDY55_30245"
                     /pseudo=""
     CDS             220..>651
                     /locus_tag="QDY55_RS30250"
                     /old_locus_tag="QDY55_30245"
                     /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            689..1207
                     /locus_tag="QDY55_RS30255"
                     /old_locus_tag="QDY55_30250"
     CDS             689..1207
                     /locus_tag="QDY55_RS30255"
                     /old_locus_tag="QDY55_30250"
                     /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_000067500.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNNEFRRLGESVSEAVTSNE
                     TKIRDAIALFTASTEESLEKHREGVKEAMMQHRRDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQANLEEIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            1214..1447
                     /locus_tag="QDY55_RS30260"
                     /old_locus_tag="QDY55_30255"
     CDS             1214..1447
                     /locus_tag="QDY55_RS30260"
                     /old_locus_tag="QDY55_30255"
                     /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_000137445.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(1782..2666)
                     /locus_tag="QDY55_RS30265"
                     /old_locus_tag="QDY55_30260"
     CDS             complement(1782..2666)
                     /locus_tag="QDY55_RS30265"
                     /old_locus_tag="QDY55_30260"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001439342.1"
                     /GO_function="GO:0005525 - GTP binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="GTPase"
                     /protein_id="WP_024133415.1"
                     /translation="MENNTQGIKLIKEAVDVLPKEIRKSVYNKIRNVINYEPVIGIMGK
                     TGAGKSSLCNSIFKGNVCAVSDVEACTRKVQELIISFGDRTIKIIDIPGVGENEAKDIE
                     YEELYKNLLPELDLVLWVVKGDDRAFSADEHFYKNVLKPVGGDEKVLFVLNQVDKIEPF
                     REWDEEKHQPSPSQQINIRKKEEYLIERFGFTKHPVISVSANEGYNISRLVEAIVRSLP
                     KEAQSGVVHQVKDEIKTKEIVETAKDGFADTVDRAIDDIIDTVLPKPIASVAKVAKKAI
                     VSVAKSVWGLIFG"
                     /name="GTPase"
     gene            complement(2702..3136)
                     /locus_tag="QDY55_RS30270"
                     /old_locus_tag="QDY55_30265"
     CDS             complement(2702..3136)
                     /locus_tag="QDY55_RS30270"
                     /old_locus_tag="QDY55_30265"
                     /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_089650385.1"
                     /translation="MGFWDSIKNAAIKAKCGVGIHGGNYKLIDGETCKYSKLCPDCNRT
                     IQKEQHKYGEENYKYDFKCTTVKKCIDCGAEQEGERHERFVEIAVDDYCNVKERCVRCF
                     TERVHGKRHNWYLSGSSDTYRHYKCSVCGEEKEERKTSFR"
                     /name="hypothetical protein"
     gene            complement(3364..4176)
                     /locus_tag="QDY55_RS30275"
                     /old_locus_tag="QDY55_30270"
     CDS             complement(3364..4176)
                     /locus_tag="QDY55_RS30275"
                     /old_locus_tag="QDY55_30270"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000549943.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EcsC family protein"
                     /protein_id="WP_000549944.1"
                     /translation="MHLEEGDLRALERAVELLEQDTITETLTQLVGTPIDYLMSKLPKG
                     AEEQIYSLVEKSLHKAADAALWSLDNEPNRIASTKTNKFFAAVSGAIGGAFGFSALAIE
                     LPVSTTIMLRSIADIARSEGFELDNIDTKLACLEVFSLGGPSDDDDAANTAYYATRSLT
                     AEIVQDLSKEISNIAVKNASSVQTGKWLASLIEKVATRFGIVITEKMAAQVVPVIGALT
                     GATLNTMFTDYYQDMARGHFIVKRLEKKYGNELIKAEYIKISSKLTNS"
                     /name="EcsC family protein"
     gene            complement(4495..4653)
                     /locus_tag="QDY55_RS30490"
     CDS             complement(4495..4653)
                     /locus_tag="QDY55_RS30490"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /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_071529495.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDKAPLAAATGNWTRWIEIL
                     RVLEVVA"
                     /name="replication initiation protein"
     gene            complement(5312..5503)
                     /locus_tag="QDY55_RS30280"
                     /old_locus_tag="QDY55_30275"
     CDS             complement(5312..5503)
                     /locus_tag="QDY55_RS30280"
                     /old_locus_tag="QDY55_30275"
                     /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_042634456.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENH"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          5153..5231
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.8899999999999995e-34"
     Typing          complement(4582..5139)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.036"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2..1551
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.473"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          5536..5879
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.391"
                     /coverage="97.0"
                     /evalue="6.599999999999999e-67"
ORIGIN
        1 atgatagtta aatttcatgc caggggaaaa ggtggtggca gtggtccggt tgattacctg
       61 ctggggaggg agcgtaaccg cgaaggcgca acggtgcttc agggtaatcc ggaagaagtc
      121 cgggaactca tcgatgccac gccatttgcg aagaaataca cgtccggtgt tctgtcgttc
      181 gcggagaagg agctgccgcc gggaggacgt gaaaaagtga tggcgagctt tgagcgtgta
      241 ctgatgcccg gtctcgaaaa aaatcagtac agcatcctgt gggtggagca ccaggacaag
      301 ggacggcttg agctgaattt tgtcattccg aacatggagc tacagaccgg aaaacgcctc
      361 cagccgtact acgaccgcgc agacaggcct agaattgatg cctggcagac gctggtaaat
      421 caccattacg ggctgcatga cccgaacgcc ccggagaacc gcaggacgct gacactccct
      481 gataacctgc ctgaaacgaa acaggcgctt gctgagggcg tcacgcgagg tatagatgca
      541 ctttaccatg ccggagagat aaaaggccgt caggatgtga ttcaggcgct cactgaggcg
      601 gggctggaag tggtcagggt gacgcgaagc agtatcagca ttgcagatcc gaacggcggg
      661 aagaatatca ggctgaaagg agcattttat gagcaatctt ttgcagacgg gcgcggagtt
      721 cgagaaaaag ctgaaagaga gagccgaatc tacagagaaa atgctgaaca acgagttcag
      781 gaggctcggc gaatctgtaa gcgaggctgt gacatcaaac gagacgaaaa tcagagacgc
      841 tatagccctg ttcacagcct cgacagagga atcgctggaa aaacaccggg aaggggtgaa
      901 agaggcgatg atgcagcaca ggagggacgt gttaaagctg gcagggaata cgggcatgat
      961 gttactgggg atagtctttc tcctgtttac cgcgagtggc gggacgctct ggtatcttgg
     1021 agggaggata caggcgaacc tggaagaaat caggaagcag gaagagacat tgcagaaact
     1081 gaacgcgaag acatggggcg tggagtttgt gcaggacggg aacaggaaat tccttgtcct
     1141 tccgtacggg aaatcagcgg aggtgattcc ctttcagggg aaagagtggg tacatctgaa
     1201 ggagtgacac agagtgacag agctggaaac acatttgctg aacgccttag agcagctgca
     1261 acaggactat atgcagcggc tgagcgaatg ggagagcgcc ttcgtggaat tgcagaagat
     1321 gttttcgctt acgcaacggg acaacgcgat gctgaacgag cgggtcatgc agttgagtca
     1381 gcaggtgcag cacttgagcg agcagacaga acgcttgagc cagttataca gcgagaactg
     1441 gagataagag aggaacggct gatacaggag cgcgaacatg tgttatccct ggaacgggag
     1501 cgtcagccgg aaatacagga acgcacgctg gatggccctt cgctgggatg gtgaaaccat
     1561 gaaaaatggc aggttcattg gattaaggcg gactaatgtg ctctgtgcca tctggttgca
     1621 taggtattca tacggttaaa atttatcagg cgcgatcgcg gcagtttttc gggtggtttg
     1681 ttgctatttt tacctgtctg ctgccgtgat cgcgctgaac gcgttttagc ggtacgtaca
     1741 aactgttgtt atgttaaata ctgatgggct ttcctgattg attatccgaa gatcaatccc
     1801 caaacacttt tagctacaga aacaatggct ttcttggcga ctttagccac tgacgctatt
     1861 ggtttaggta gtacggtgtc tattatatca tcaatagctc tatctacggt gtctgcgaac
     1921 ccgtcctttg ccgtttctac aatttctttt gtttttattt cgtcttttac ttgatgcacc
     1981 actccgctct gtgcttcctt tgggagcgat cttactattg cctccactaa ccttgaaatg
     2041 ttataacctt cattcgcaga tacagatata acgggatgtt tggtaaaacc gaatcgttct
     2101 attaagtatt cttccttttt tctaatattt atttgttgtg agggtgatgg ttggtgtttt
     2161 tcttcatccc attcgcggaa tggctcaatc ttgtcgactt ggtttaaaac aaacaacact
     2221 ttttcatcac caccaactgg ttttaaaaca tttttataaa agtgctcatc agctgaaaat
     2281 gctcgatcat cacctttaac aacccaaagc accagatcta attctgggag aagattttta
     2341 tacaactctt catattctat atctttagct tcattttcac ctacacctgg tatatctatt
     2401 attttaattg ttctatcacc aaatgaaatt attaattcct gaacctttct cgtgcatgct
     2461 tctacatcac tcactgcaca tacattacct ttaaagatag aattacatag gctggattta
     2521 ccagcgccgg ttttacccat aatccctatt actggttcgt aattaataac atttctaatt
     2581 ttgttataga cagacttgcg aatctcttta ggtagaacat ccacagcttc tttgattaat
     2641 tttatacctt gcgtattgtt ttccatagtt actattttcc tcattttgtt gttcatatga
     2701 attaacggaa gcttgttttt ctttcttctt tttcttcccc gcatacagaa catttgtaat
     2761 ggcgataggt atcagaactc ccactaagat accaattgtg tcttttacca tgaactcgct
     2821 ctgtaaaaca tctcacgcat ctttctttca cattgcaata atcatcgact gcaatttcaa
     2881 caaatctttc atgcctttcg ccttcttgtt cagcgccaca gtcgatacac ttttttacag
     2941 ttgtgcactt gaaatcgtat ttataatttt cctctccgta tttatgctgt tctttttgta
     3001 tagtgcgatt gcagtcaggg catagtttag aatatttaca agtctcacca tcaataagct
     3061 tatagtttcc tccgtgtata cctaccccac acttagcctt gattgctgca ttttttatgc
     3121 tatcccaaaa gcccatggaa aaatctccct acgattagtt gatataagtt gaacaattca
     3181 tcgacatgat tatacacgta tagtgtgtgg atatataaaa atgagtatgg atttatgctc
     3241 tgtataatgt tgttgttata ttaaatatag agctgaaaaa gtgggggcac tggataaact
     3301 tcgtgttttt cccgcaaaga tagtattgga aagtcattgt ctaattcatc caagataaat
     3361 attttacgaa tttgtgagtt tgcttgagat ttttatatat tcagccttta ttaactcatt
     3421 gccatatttt ttctcgagcc ttttaacaat gaaatgacct cgagccatat cttgataata
     3481 gtcggtaaac attgtgttta atgtggctcc agttagtgct ccaataacgg gaacgacttg
     3541 agctgccatt ttttccgtaa taactatacc aaatcttgtt gcaacttttt ctattaacga
     3601 agctaaccat tttcctgttt gtactgaaga tgcgtttttg acagcaatgt tagaaatttc
     3661 tttggataaa tcttgtacga tctcggcagt caaacttctt gttgcatagt atgcagtatt
     3721 agctgcatca tcgtcatcag atggtcctcc caaggaaaac acctctaagc aggccagttt
     3781 ggtatcaata ttatctagct caaaaccttc acttcttgct atgtcagcaa ttgaacgaag
     3841 cataattgtc gttgaaaccg gtaactcaat tgctaatgca gaaaagccaa aagcgccacc
     3901 aatggctcca gatacggccg caaagaattt atttgtctta gttgatgcta ttcggttagg
     3961 ttcattgtct agactccata aggctgcatc agcagctttg tggagagatt tttctactag
     4021 actataaatt tgctcttctg cccctttggg aagtttactc attaagtaat ctattggggt
     4081 tccaactaat tgggttaatg tttcagtaat tgtatcttgt tctaataatt ctacggccct
     4141 ttctaaagcc cgcagatctc cttcttcaag atgcatataa tgaatccttt atgaatcaat
     4201 cgatagtcta cttttgtaag tgattcgtct tgggagctta ccttgagcga gttcagtgat
     4261 tcaataggcg agatgccgac atcattgttg tctgtgaagc aggagtgatg aaaagatcaa
     4321 aggatcctct tgtgatcctt tttttctgcg cgtaatctgc tgcctgtaaa caaaaaaacc
     4381 accgctacca acggtggttt gtttgccgga tcaagagcta ccaactcttt ttccgaaggt
     4441 aactggcttg gtggagcaca gataccaaat actgtccttc tagtgtagcc gcagttaggc
     4501 caccacttca agaactctta atatctcaat ccaccttgtc cagttaccag tggctgctgc
     4561 cagtggcgct ttgtcgtgtc ttaccgggtt ggactcaaga cgatagttac cggataaggc
     4621 gcagcggtcg ggctgaacgg ggggttcgtg cacacagccc agcttggagc gaacgaccta
     4681 caccgaactg agataccaac agcgtgagct atgagaaagc gccacgcttc ccgaagggag
     4741 aaaggcggac aggtatccgg taatcggcag ggtcggaaca ggagagcgca cgagggagcc
     4801 accaggggga aacgcctggt atctttaagt cctgtcgggt ttcgccacct ctgacttgag
     4861 cgtcaatttt tgtgatgctc gtcagggggg cggagcctat ggaaaaacgc caggggcgcg
     4921 gcctttttcc tggttttgcc tttttgctca catgttcttt ccggccttat cccctgattc
     4981 tgtgggtaac cgcattaccg tctctgagtg agctgatacc gctcgccgca gccgaacgac
     5041 cgagcgcagc gagtcagtga gcgaggaagc ggaagagcgt aggcatttgc attttctcct
     5101 tacgcatctg tgcggcattt cacaccgtcc atggcgcact tttcatacaa tccgcactga
     5161 tgtcgcatag ttaagccagt atacactccg ctagcgctac gtgactggtt cagggcttcg
     5221 ccccgaaacc ccctgacgcg ccctgacggg cttgtctgct cccggcatcc gctcacagac
     5281 aagctgtgac cgtctccggg agctgcatgt gtcagtggtt ttcaccgtca tccccgaagc
     5341 gtgcgaggca gctgcggtaa agctcatcgg cgtggtcgtg aagcgattca cagatatctg
     5401 cctgttcatc cgcgtccagt tcgttgagct tctccagcag cgttaatgtc tggcttctga
     5461 taaagcgggc catgttaagg gcggtttttt cctgttttgt cactgatgcc tccgtgtaag
     5521 ggggatttct gttcatgggg gtaatgatac cgatgaaacg cgagaggatg ctcacgatac
     5581 gggttactga tgatgaacat gcccggttac tggaacgctg tgagggtaaa caactggcgg
     5641 tatggatgcg gcgggtctgc ctgggggagc cggttgcccg ttccggaaaa ctgccgacac
     5701 tggcaccgcc gttactgcgt cagctggccg ccatcggaaa taacctgaat cagacagccc
     5761 gtaaggtgaa cagcgggcag tggtcttccg gtgaccgggt tcaggtggtg gccgcactga
     5821 tggccatcgg ggatgagctg cgccggctgc gtctggctgt cagggaacag ggggcgcggg
//
