LOCUS       NZ_CP122590             5775 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC6335 plasmid unnamed2, complete
            sequence.
ACCESSION   NZ_CP122590
VERSION     NZ_CP122590.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32549676
            Assembly: GCF_030013005.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5775)
  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 5775)
  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                   :: 260x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030013005.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 05:27:29
            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)                     :: 5,662
            CDSs (total)                      :: 5,534
            Genes (coding)                    :: 5,336
            CDSs (with protein)               :: 5,336
            Genes (RNA)                       :: 128
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 97
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 198
            CDSs (without protein)            :: 198
            Pseudo Genes (ambiguous residues) :: 0 of 198
            Pseudo Genes (frameshifted)       :: 83 of 198
            Pseudo Genes (incomplete)         :: 121 of 198
            Pseudo Genes (internal stop)      :: 29 of 198
            Pseudo Genes (multiple problems)  :: 27 of 198
            Pseudo Genes (short protein)      :: 1 of 198
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122590.1.
            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..5775
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC6335"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed2"
                     /geo_loc_name="Netherlands"
                     /collection_date="2021"
                     /collected_by="IMM_DI04"
     gene            587..751
                     /locus_tag="QDY30_RS25635"
                     /old_locus_tag="QDY30_25635"
     CDS             587..751
                     /locus_tag="QDY30_RS25635"
                     /old_locus_tag="QDY30_25635"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000968835.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000968835.1"
                     /translation="MMDKDTTTLKRTLAHNRAFSDNINRSGIAWCYNTEIVLAACEAIE
                     AELQRRGCL"
                     /name="hypothetical protein"
     gene            1122..1634
                     /locus_tag="QDY30_RS25640"
                     /old_locus_tag="QDY30_25640"
     CDS             1122..1634
                     /locus_tag="QDY30_RS25640"
                     /old_locus_tag="QDY30_25640"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001445155.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001276096.1"
                     /translation="MSARARKAGKRNQSERRQDLIEKLWEDDEIDTWHRLENDGYSTVP
                     RYLPLIGDLMDGLSKGSPLSTTYLALWFRVSDEGLIEIRDKAALAFESGFASERGVTTW
                     AGRMKKLKELGFISCREGSTGEFHYVLIVHPLVAVKKLLDEGIIPKGKTYNILSERVIE
                     VGASWEG"
                     /name="hypothetical protein"
     gene            1635..2129
                     /locus_tag="QDY30_RS25645"
                     /old_locus_tag="QDY30_25645"
     CDS             1635..2129
                     /locus_tag="QDY30_RS25645"
                     /old_locus_tag="QDY30_25645"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000929317.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000929317.1"
                     /translation="MAGTVWRDIRTGETVFPMGHLHPQRCCVDVNGTSVDIEISFGFHV
                     FTDEKQTGMLMKFKEEQRFFCRERYEGSKTIVHRILTAIENGEYITAFISKGQGQRYYH
                     LSHHDDFILMEIRKPQDRNNSLRIHVVTAYTLDEWGTVNKGRNLRFRYVLEQRLQGKKI
                     V"
                     /name="hypothetical protein"
     gene            complement(3676..3867)
                     /locus_tag="QDY30_RS25650"
                     /old_locus_tag="QDY30_25650"
     CDS             complement(3676..3867)
                     /locus_tag="QDY30_RS25650"
                     /old_locus_tag="QDY30_25650"
                     /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            3932..4255
                     /locus_tag="QDY30_RS25655"
                     /old_locus_tag="QDY30_25655"
     CDS             3932..4255
                     /locus_tag="QDY30_RS25655"
                     /old_locus_tag="QDY30_25655"
                     /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="plasmid mobilization relaxosome protein MobC"
                     /protein_id="WP_000955995.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIERELRSLRQVVREHGAR
                     DDS"
                     /name="plasmid mobilization relaxosome protein MobC"
     gene            4464..>4895
                     /locus_tag="QDY30_RS25660"
                     /old_locus_tag="QDY30_25660"
                     /pseudo=""
     CDS             4464..>4895
                     /locus_tag="QDY30_RS25660"
                     /old_locus_tag="QDY30_25660"
                     /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            4933..5451
                     /locus_tag="QDY30_RS25665"
                     /old_locus_tag="QDY30_25665"
     CDS             4933..5451
                     /locus_tag="QDY30_RS25665"
                     /old_locus_tag="QDY30_25665"
                     /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_000067503.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVLFLFTVSG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVLPYGKSATVIPYQ
                     EKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            5458..5691
                     /locus_tag="QDY30_RS25670"
                     /old_locus_tag="QDY30_25670"
     CDS             5458..5691
                     /locus_tag="QDY30_RS25670"
                     /old_locus_tag="QDY30_25670"
                     /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_000137441.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLSEWESAFVELQKMFSLTQRDNA
                     MLNEQVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          3501..3584
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.07e-36"
     Typing          2838..3059
                     /name="rep_cluster_2392"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.825"
                     /coverage="87.0"
                     /evalue="1.42e-85"
     Typing          4246..5774
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.683"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 atggcccttc gctgggatgg taatcagaga caggctaaaa tgttgtcagc gcgtttccgg
       61 tgcatttttt gggataatgg ttggttcggg ggcaccggga acgcgcttca gtcagacctt
      121 gctgaaaaca caggaacgcg ttaaaacgca tacgggcgcg attctggtgt gtcttttgtt
      181 gctgtgtttt gcctctattg ccagatcgcg ctcattcccc tgaacttctg ttttcccgct
      241 ccggtccccg tcttcttcgc ttccgaaagc atgaaaaaaa tccgtttcag ctgtctctgg
      301 ctggcaattc ctgcgtgatt cacatggctg catagctatg catgtggtta aaatttaccg
      361 ggtgcgatcg cggcagtttt tcgggtggtt tgttgccatt tttacctgtc tgctgccgtg
      421 atcgcaccga acgcgtttct gcggtgcggg caacggatgt tatggtaaat attggtgctc
      481 tgggatgaag cgaaaatagg ctttttttcg ctattttagc ctgttcagga acggcaagag
      541 taaatatctg ggagcatgaa gctcgttaac ctgaatggag atcctgatga tggacaaaga
      601 taccaccacc ctaaaacgca ctttggctca taatcgagcc tttagcgata atattaaccg
      661 cagtggcata gcttggtgct ataacactga gattgtactc gctgcttgtg aggcgattga
      721 agccgaacta caacggcgag gatgtttgta acaataagaa aacccgcatc agcgggtttt
      781 ttagtctctg agacgcgcta ccgctaaatt atttttctct ctatccgccc tggcttgccc
      841 cctacaaccc catggagcac aaggagcaca gggagaacca tcgagcacaa cgagcacaat
      901 gagcaccgcc ttcctcttat aaatcattat taatcatata attaaacaac ttcattgtaa
      961 tatatattac tttttatgtt tttaaatgta atgtttattg cgatttagct tgtttttaac
     1021 tctatttttt cagatgagaa caagctgcca gcaatgaata actatttgat tttattggtt
     1081 ttttcaataa attagtgtcc atagacaaac gggagacgac tatgtccgca agagcaagaa
     1141 aagcaggtaa gagaaatcag tcagaacgac gtcaggattt gattgaaaaa ttgtgggaag
     1201 acgacgaaat cgatacttgg catcgacttg aaaatgatgg gtactcaaca gttccacgtt
     1261 atttgccttt gataggcgat ctcatggatg gtctgtcaaa aggatcacca ttatcaacaa
     1321 cctacttggc tttatggttc agggtttctg atgaggggtt gattgaaata agagataaag
     1381 cagcactggc ttttgaatca gggttcgcta gtgaaagagg cgtaactaca tgggcaggga
     1441 gaatgaaaaa gctaaaagaa ctggggttca tatcctgtcg tgaaggcagc accggtgaat
     1501 ttcattacgt gttaattgtt cacccattag ttgcagtcaa aaagctgctt gatgaaggga
     1561 ttatccctaa aggaaagact tataacattt tgtcggagcg tgtaattgag gtgggagcct
     1621 cttgggaggg ttaaatggcg ggcacagtat ggcgtgacat aagaacggga gagactgttt
     1681 ttcctatggg gcacctgcac cctcagaggt gctgtgttga tgtaaacggt acttctgtag
     1741 atatagaaat tagttttggt tttcatgttt ttactgatga aaaacaaacc ggaatgctga
     1801 tgaaatttaa ggaggaacag aggttttttt gtagggaacg ctatgagggc agcaaaacta
     1861 tcgttcacag aatacttaca gcgatagaaa acggtgaata cattacagca tttatttcaa
     1921 aggggcaggg gcagcggtat taccatctta gccatcatga tgacttcatt ttgatggaaa
     1981 taagaaagcc tcaagataga aataattctt tgcgtattca tgttgttaca gcttacacgc
     2041 ttgatgaatg ggggactgta aataaaggac gtaacctgcg gtttagatat gtgctggaac
     2101 agcgactgca gggaaagaag attgtgtaaa aaacaaaaag cgcctaaggc gcctttgttt
     2161 tttgcagaat ttcggtctgg cctttcgtta tcccgctcac aggctgggag ggtgtgaccc
     2221 ccggcatcag cacccctctc tcgaggttcc ggtttgtgct gacaacatta gtatcctatt
     2281 ccacatgttc gttgtcaaac tagcgtactt tttggtgttc attggtgttt ataggttgtc
     2341 atttaccctc tttgtggtta taagtgttta taggttttca ttgtttttta taggtgttca
     2401 tatgaagttg cttgatagta atgaagtgtg tgagctctta ggcatcagta agtccacttt
     2461 gtatcgttgg tgcggggtgt ctgaggattt ttctggcttg ggtctaagta gcggtcttcc
     2521 tcaggctaac gctactcaga actctttagg cagggaaaat aggctcgtta ggagggaatt
     2581 acagcaaaac gctctcggtg tcgaagagac gccaagcgac ttccctcgtc ctttcaagat
     2641 cggtcgttcg tttaaatgga aagacgccga aattatggct tggcttgaaa cgcgacgcgt
     2701 ttgattgata gatcttcttg agatcatttg gatctcgtcg tagtcttttg tcctgtaaac
     2761 gaaaaaacca ccatggcagg tggtttttcg aaggttattt aatcctggca gattgaataa
     2821 ccgtggtaac agccttgtgc gagacgtgtc accaaatctg tcctttcagt gtagcctcac
     2881 taaggccacc acttcaagaa ctttgaatac atctctcgca catcctgttt accaatggct
     2941 accgccactg gcgatttttc gtgtctgttc cgggttggac tcaagatgat agttaccggg
     3001 acaacgtggt agtcgggctg aacggggggt tcttgcatac agcccagctt ggagcgaact
     3061 gtctaaacgg aacgggacgt ggtgatttag gtaaagcttc caccacaaca cggatgccgc
     3121 aggacgggaa caggagagcg caagagggag ccgccagggg gaaacgcctg gtatctttaa
     3181 gtcctgtcgg gtttcgccac ctctgacttg agcgtcgatt tttgtgatgc tcgtcagggg
     3241 ggcggagcct atggaaaaac gccagcggcg tggccttctc tgggttcttg ttttttgctc
     3301 acatgtttct tttggtgtta tcccctgatt ctgtggataa ccgcattacc gtctttgagt
     3361 gagctgatac cgctcgccgc agccgaacga ccgagcgtag cgagtcagtg agcgaggaag
     3421 cggaagagcg tcggaagttg cattttctcc ttacacatct gtgcggcatt tcacacccgg
     3481 catggcgcac ttttcataca atccgcactg atgccgcatg gttaagccag tatacactcc
     3541 gctatcgcta cgtgactggg tcatggctgc gccccgacac ccgcaaggtc aacggcctga
     3601 cgcgccctga cgggcttgtc tgctcccggc atccgctcac agacaagctg tgaccgtctc
     3661 cgggagctgt atgtgtcaga ggttttcacc gtcatccccg aagcgtgcga ggcagctgcg
     3721 gtaaagctca tcggcgtggt cgtgaagcga ttcacagatg tctgcctgtt catccgcgtc
     3781 cagttcgttg agcttttcca gcagcgttaa tgtctggctt ctgataaagc gggccatgtt
     3841 aagggcggtt ttttcctgtt tagtcactga tgcctccgtg taagggggga tttctgttca
     3901 tggggtaatg ataccgatga aacgcgagag gatgctcacg atacgggtta ctgatgatga
     3961 acatgcacgg ttactggaac gctgtgaggg taaacagctg gcggtatgga tgcggcgggt
     4021 ctgtctgggt gagccggttg cccgttccgg gaagctgccg acactggcac cgccgttact
     4081 gcgccagctg gctgccatcg ggaataatct gaatcagacg gcgaggaagg tgaacagcgg
     4141 gcagtggtct tccggtgacc gggttcaggt ggtggccgca ctgatggcca tcgagagaga
     4201 gttgcgcagc ttacggcagg tcgtcaggga acatggagcg cgggatgata gttaagtttc
     4261 atgccagggg aaaaggcggt ggcagtggtc cggttgatta cctgctggga agggagcgta
     4321 accgggaagg ggcaacggtg cttcagggta atccggaaga agtccgggaa ctcatcgatg
     4381 ccacgccatt tgcgaagaaa tacacgtcag gtgttctgtc gttcgcggag aaggagctgc
     4441 cgccgggagg acgtgaaaag gtgatggcga gctttgagcg tgtactgatg cccggtctcg
     4501 aaaaaaatca gtacagcatc ctgtgggtgg agcaccagga caagggacgg cttgagctga
     4561 attttgtcat tccgaacatg gagctacaga gcggaaaacg cctccagccg tactacgacc
     4621 gggcagacag gccgagaatt gatgcctggc agacgctggt taatcaccat tacgggctgc
     4681 atgaccccaa cgccccggag aaccgccgga tactgactct ccctgataac ctgccggaaa
     4741 cgaaacaggc gcttgcagag agcgtcacac gcgggataga cgctctttat catgtcgggg
     4801 agataaaagg ccgtcaggat gtgattcagg cgctcacaga ggcagggctt gaagtggtca
     4861 gggtgacgcg aagcagtatc agcattgcag acccgaacgg cgggaagaat atcagactga
     4921 aaggagcatt ctatgagcaa tcttttacag acgggcgcgg agttcgagaa aaagctgaaa
     4981 gagagagccg aatctacaga gacaatgctg aacgacgagt tcagcaagct cgaaaaatct
     5041 gtaagcaagg ctgtgacatc aaacgagacg aaaatcaaag acgctatagc cctgttcaca
     5101 gcttcgacag aggaatcact gaaaaaacac cgggaagggg tgaaagaggc gatgatgcag
     5161 cacaggaagg acgtgttaaa gctggcaggg aatacgggca tgatgttact ggggatggtc
     5221 cttttcctgt ttaccgtgag tggcgggacg ctctggtatc ttggcgggcg gatacaggcg
     5281 aacctggaag aaatcaggat acaggaagaa acattgcaga aactgaacgc gaagacatgg
     5341 ggcgtggagt ttgtgcagga cgggagaagg aaatttctgg tccttccgta cgggaaatcg
     5401 gcaacggtga ttccctatca ggagaaggac tgggtacaac tgacggagtg acacagagtg
     5461 acggagctgg aaagacattt gctgaacgcc ttagagcaac tgcaacagga ctatatgcag
     5521 cggctgagcg aatgggagag cgccttcgtg gaattgcaga aaatgttttc gcttacgcaa
     5581 cgggacaacg cgatgctgaa cgagcaggtc atgcagttga gtcagcaggt gcagcacttg
     5641 agcgagcgga cagaacgctt gagccagtta tacagcgaga acaggagata agggacgaac
     5701 ggctgataca ggagcgcgaa catgagttat ccctggagcg tgagcgccag ctggaaatac
     5761 aggaacggac actgg
//
