LOCUS       NZ_CP122598             5145 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC6335 plasmid unnamed10, complete
            sequence.
ACCESSION   NZ_CP122598
VERSION     NZ_CP122598.1
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 5145)
  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 5145)
  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
            CP122598.1.
            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..5145
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC6335"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed10"
                     /geo_loc_name="Netherlands"
                     /collection_date="2021"
                     /collected_by="IMM_DI04"
     gene            1519..2426
                     /locus_tag="QDY30_RS28225"
                     /old_locus_tag="QDY30_28235"
                     /pseudo=""
     CDS             1519..2426
                     /locus_tag="QDY30_RS28225"
                     /old_locus_tag="QDY30_28235"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009440807.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            complement(2619..3017)
                     /locus_tag="QDY30_RS28230"
                     /old_locus_tag="QDY30_28240"
     CDS             complement(2619..3017)
                     /locus_tag="QDY30_RS28230"
                     /old_locus_tag="QDY30_28240"
                     /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_001222911.1"
                     /translation="MRISNIEWLKKRIEFIRKLGKQTARQRQIIDLLDNEDRLTEQERK
                     LLHVLATAEKNDLQAQESERKQAIQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDMLLQRLKPIKYDLDTCPNPDA"
                     /name="hypothetical protein"
     gene            3194..4120
                     /locus_tag="QDY30_RS28235"
                     /old_locus_tag="QDY30_28245"
     CDS             3194..4120
                     /locus_tag="QDY30_RS28235"
                     /old_locus_tag="QDY30_28245"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_002430978.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPDRGGAKKDSGNLT
                     PTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYYRHLEQARMVGHDIREWLDTPVKQHELVRRLQHDIAREHGFD
                     MRDGVSRQNRTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            4123..4656
                     /locus_tag="QDY30_RS28240"
                     /old_locus_tag="QDY30_28250"
     CDS             4123..4656
                     /locus_tag="QDY30_RS28240"
                     /old_locus_tag="QDY30_28250"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001590995.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISLDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTMLDRNYNATAAVYQKVVTLED
                     KLAEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            complement(4722..4931)
                     /locus_tag="QDY30_RS28245"
                     /old_locus_tag="QDY30_28255"
     CDS             complement(4722..4931)
                     /locus_tag="QDY30_RS28245"
                     /old_locus_tag="QDY30_28255"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001618649.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001618649.1"
                     /translation="MAKLGENTPHIIDATVDFMASSQAFREYLRKLPPDHTIPPDLTDE
                     HVPLYIRRLEYYRLLYRPKQTESY"
                     /name="hypothetical protein"
     Typing          1520..2247
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.61"
                     /coverage="88.0"
                     /evalue="0.0"
     Typing          3195..4117
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atgtatggaa tggaagtgag ctttaaggtt tcagctctaa aaaataaaat atttattagt
       61 tggttggttg ttgttcttgt tctgtatgta tataaacact atcgacatat tatgaccggg
      121 aacattcctt accccctctg cgctctcaga gggttttttt tgtcattaat taataatgaa
      181 ctgaaatgca gttccgatac ctccatttgc acattatccc tgacatatgg taccggaatc
      241 gcattaattt tatgttataa gagtttattt ttaatgtcca gatggtttaa tggtatttat
      301 atgtaattag ctgtatggat agtactgttt ttattgtata acttgttgtt ttttattgtt
      361 ttttgtgtgg tgtgctaatc tttaagttat aaaaaaaccc cttggaacac aggggcaaaa
      421 gtaaggaaaa caaatggatg ctcagtttgt gtgacacttt aaactaatgg aactatagag
      481 tggaggttgt tacagtcgct tttataaaac agcaaccagt ttttttcaat agtctgatga
      541 tggttgtgac agttttgtga tattgttcaa aatgtttctt gttgaatgtt tgttttttgg
      601 tctattggtg tctggtttta ttttttctgc tattacatat caagaaatgt gattggtgta
      661 gcaagagtgg aatgcgatgt ggataaacta attggttgtc gaatctaatt tacttagaaa
      721 actacacttg tttttgtgta tgaatttagt gaatttgtct gtctatgtgt tttcgtgcat
      781 ttataaatcc ttcgtcagga tcttaaattt agtgttgaat atgtagggcc tgtacggtaa
      841 ttattattta gcgtagctac ttcatcgttg ttcgaacaca accaacaacc tgtaattgtt
      901 gtttctcttg gttccccact tttgtggggt tttttatctc ttccgtgcat cgtaaagcgc
      961 ggactccttc tggaaaggtt gttttagggc atcactgagg cattttttgc gtttgtgaat
     1021 attgagcatc cgataactaa aatatttccc atagactctg attcttgcca ccgaccccag
     1081 gtcggttttt tttgtcctgg cgagatgtga agtttggaaa caggaaaccc cgtcagagcg
     1141 ccacgcacca ggggagaaaa cttgtcgttt tgagccgttc ggtgttcaga acgcacgaaa
     1201 ccgatcgcac atcgctttcg tgcatagtta tgcaacgccc tgaaaacgat tctgacgcat
     1261 ttttctggtt cagcctggtg tttccttgtc tttttgcgtt ttttgcgtca gaaagcgatt
     1321 gagggcgttt tatggggtgc gtacaacggg agttatggta aatggatcgg atttgcggga
     1381 aggctcgaca ggttttgtcg ttgggggtag tgtaagcgac tgaaaaacaa acgcccctga
     1441 aattcgtgtc tatccgccaa gactttcacg aaaatacagg ggcgatgtcg gtcgataacc
     1501 tggaaggaat cgtaacacat gagcgccgcg cttcaatact tcgaagaaaa tttaccccac
     1561 cgtccctatc acacggatga tctcgctttc ggccttcgta tctccggcaa agggcgcgcg
     1621 cttcttgcac ggtatatcca gcagaaccag cctcatgcac agttctggct ggtttttgac
     1681 gttgaccgcg agggggctgc gattgactgg agcgaccgga acgctcccgc gccgaacatc
     1741 accgttaaaa atcctgtgaa cggacacgct cacctgctct acgcactcaa catcgccgtg
     1801 agaaccgcgc ctgatgcctc ggttaaggcg ctgaaatatg ccgcagcggt tgaacgttcg
     1861 ctgtgtgaga aactttgtgc ggatgtgaac tacagcggcc tgatttgcaa aaatccgttc
     1921 cacctggaat ggctggtgat ggagtggcgc gaggaagcct ataccctcga tgaactggct
     1981 gattatctcg atttgagcgc ctcagcgcgc cgtagcatcg ataaacatta cgggatgggg
     2041 cgaaactgcc acctgttcga aatgacgcgc aaatgggctt acagggcgat tcgtcagggc
     2101 tggcctgaat tctcacagtg gcttgatgcc gtgattcagc gtgtcgaaat gtacaacgca
     2161 tcgcttcctg ttccgctttc accagctgaa tgccgggcta ttggcaggag cattgcgaaa
     2221 tacacgcata gaaaattctc gccagaaggg ttttccgctg tacaggccgc acgcggtcgc
     2281 aaggggggat cgctaaaggc gaagcctacg aggacaagcg tttcatggcg ttatgtatgc
     2341 tggagaatgg atattctcag aaagctattg cggcgatgct gaatgtacat cgtaatacga
     2401 tccgtaattg ggcaatgcac aaatagcctt atcagataac agcgcctttc cggcggtttt
     2461 ttgagcagct attttttggg tggtttctgc ttgtcagccc agcaatggtg cggcttttcg
     2521 cttgattgag gtggtagtgc tcgccgcagt ctcatgaccg agcgtagcga gcgaatgagc
     2581 gaggaagcac cagggcaccg gaacgtgaac gggaacactt acgcgtctgg gtttgggcat
     2641 gtgtctagat cgtacttaat gggtttaagt ctttgtaata acatgtcttt tttatagcat
     2701 agctcgcctg tttttgtgtc caccagtcct gcttcgatca gtagtcctgc cgcgagaaag
     2761 agccggtgat tgcgttcccg tcgttgtttc ttcccctcga ttcgtttctg gatcgcctgt
     2821 tttcgttcgc tctcctgtgc ctgtaagtcg tttttttcgg ctgttgctag tacgtggaga
     2881 agtttgcgtt cctgttctgt gagtctgtcc tcgttgtcga gcaggtcaat gatctgtctc
     2941 tgtcgtgcgg tctgttttcc gagcttcctg atgaactcga tccgtttctt cagccattcg
     3001 atgttgctga tgcgcatgtt ggtggtgctc cctggtgttt ttttgcggtg tgttgtggtc
     3061 gtgcagtata tcgcttgcgg tcggtgggtg caggggttac cttccgtact aattcgaaaa
     3121 attagaagga agcgcactta tatgtttctc tccttcgttg agaaacagtg cgctcctgcg
     3181 gagggctgaa accgtggcga cctatcacct cagcgttaaa tttggtggca agggacaggc
     3241 tgccaaccat gccgattaca tcgagcgcaa agagaaatac cgcgaccgtc aagatttgga
     3301 atattccgca cacggaaaca tgccggaatg ggccagggat aatccttccc atttctggca
     3361 ggcggctgac cagtttgaac gtgcgaacgg ttcgacctat agggaacttg aaattgcatt
     3421 accccgtgaa ctgacaccgg aacagcgcct tgaactggtg caggattttg tacgtcagga
     3481 agctggcgaa cggcacgcct ggagttttgc cattcacaat ccgaaagcga gcattgacgg
     3541 cggcgaacag cctcatgcac atatcatgat gagtcagcgt gtgaatgatg gcattgaacg
     3601 tacaccggaa cagtatttcc ggcgctataa cgccaggtat cccgaccggg gaggtgcgaa
     3661 aaaggattcc ggaaacctga cccccactca gcaaaaagag cagttgcggg aattgcgaaa
     3721 acgctgggag gtgaagcaca acgaacatat gagaaagcat ggctttgaaa ggggcttcat
     3781 tgactgccgg acgctgaaag aacagggcat tgaacgacgt cccgaagtgc atctgggttt
     3841 tgaagctgcc ggacgacttg atgatgccca gcgtcatgac atcatgcaaa aacggtctga
     3901 accggactat taccgccatc ttgaacaggc gcgaatggtc gggcatgaca tcagggaatg
     3961 gctggataca ccggttaagc aacatgaact ggtcagaagg ctgcaacatg atattgcgcg
     4021 ggaacatggc tttgacatga gagacggagt gagcagacag aaccgaactg aacctgaacg
     4081 ggttaaatca ccgtcacgtg gattttctat gggattctga acatggccag cacagaagaa
     4141 aaattactca cgctcctgtt atcggtggag catctgcaac ataccgcaat ggagcaacag
     4201 aaagctgttg ctgattctct ggctgtggca agggaaacgc ttcgcggata tcgggatatt
     4261 tctgacggtg tggcaaaaca ggtcagggat gaagtcagaa atgaggtgca gaagctggac
     4321 gtagcagggc tgataggtga gcgcatcagc ctggattttc agcggctgga agagtcagtc
     4381 gcaaacatga aggcaaacgc ggatgccctg aacagggata ttgcgacaat tcacagcaat
     4441 atcgtgcagg aatacaacac ccttaaaggg tatagctgga aatggctggg tggtgtgtca
     4501 gtggcttttc tggttatgtt ctgtgtgctc ggatggggaa tgaaaacaat gctcgacagg
     4561 aactacaacg ccacagcggc ggtgtatcag aaagttgtga cactggaaga taaactggcg
     4621 gagaaacctg tcacgggtaa gagccggaaa aactgacgcg cttcgcttgt ccaacgcctc
     4681 acggagcgcg aaaggatttc gcgaaccgtt caccgttttt ttcaatatga ttctgtctgc
     4741 tttggtcgat aaagcagtcg atagtattcc agccttcgta tatataacgg tacgtgctca
     4801 tcagtaagat ctggcggtat tgtgtgatca gggggaagtt ttctcagata ctcacgaaat
     4861 gcctggcttg atgccataaa atctacagta gcatcgataa tatgtggggt gttttcacct
     4921 aattttgcca tgatgataat ccttatatta tcacggttcg tgaatgatag ggggtcacta
     4981 ttatttatgc gttagtaaac cagaaaaaat cccccgttgg cataggggga tatgtaagga
     5041 gaaataactt cgcaggtgtt cttgtttgta taacgtgaaa agactgcacg caacttaata
     5101 agtctgccgt acttactttc agttttcaac ataaggttta taaca
//
