LOCUS       NZ_CP122774             5732 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC1738 plasmid unnamed6, complete
            sequence.
ACCESSION   NZ_CP122774
VERSION     NZ_CP122774.1
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 5732)
  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 5732)
  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
            CP122774.1.
            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..5732
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC1738"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed6"
                     /geo_loc_name="Belgium"
                     /collection_date="2021"
                     /collected_by="IMM_DI04"
     gene            1..495
                     /locus_tag="QDY55_RS30285"
                     /old_locus_tag="QDY55_30280"
     CDS             1..495
                     /locus_tag="QDY55_RS30285"
                     /old_locus_tag="QDY55_30280"
                     /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(2019..2210)
                     /locus_tag="QDY55_RS30290"
                     /old_locus_tag="QDY55_30285"
     CDS             complement(2019..2210)
                     /locus_tag="QDY55_RS30290"
                     /old_locus_tag="QDY55_30285"
                     /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            2275..2598
                     /locus_tag="QDY55_RS30295"
                     /old_locus_tag="QDY55_30290"
     CDS             2275..2598
                     /locus_tag="QDY55_RS30295"
                     /old_locus_tag="QDY55_30290"
                     /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            2807..>3238
                     /locus_tag="QDY55_RS30300"
                     /old_locus_tag="QDY55_30295"
                     /pseudo=""
     CDS             2807..>3238
                     /locus_tag="QDY55_RS30300"
                     /old_locus_tag="QDY55_30295"
                     /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            3276..3794
                     /locus_tag="QDY55_RS30305"
                     /old_locus_tag="QDY55_30300"
     CDS             3276..3794
                     /locus_tag="QDY55_RS30305"
                     /old_locus_tag="QDY55_30300"
                     /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_282870987.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTETMLNDEFSKLEKSVSKAVTSNE
                     TKIKDAIALFTASTEESLKKHREGVKEAMMQHRKDVLKLAGNTGMMLLGMVLFLFTVSG
                     GTLWYLGGRIQANLEEIRIQEETLQKLNAKTWGVEFVQDGRRKFLVIPQGKSATVIPYQ
                     EKDWVQLTE"
                     /name="MbeB family mobilization protein"
     gene            3801..4034
                     /locus_tag="QDY55_RS30310"
                     /old_locus_tag="QDY55_30305"
     CDS             3801..4034
                     /locus_tag="QDY55_RS30310"
                     /old_locus_tag="QDY55_30305"
                     /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"
     gene            4694..4858
                     /locus_tag="QDY55_RS30315"
                     /old_locus_tag="QDY55_30310"
     CDS             4694..4858
                     /locus_tag="QDY55_RS30315"
                     /old_locus_tag="QDY55_30310"
                     /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            5220..5732
                     /locus_tag="QDY55_RS30320"
                     /old_locus_tag="QDY55_30315"
     CDS             5220..5732
                     /locus_tag="QDY55_RS30320"
                     /old_locus_tag="QDY55_30315"
                     /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"
     Typing          1873..1951
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="90.0"
                     /coverage="100.0"
                     /evalue="1.29e-20"
     Typing          1204..1425
                     /name="rep_cluster_2392"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.825"
                     /coverage="87.0"
                     /evalue="1.42e-85"
     Typing          2589..4066
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="90.543"
                     /coverage="95.0"
                     /evalue="0.0"
ORIGIN
        1 atggcgggca cagtatggcg tgacataaga acgggagaga ctgtttttcc tatggggcac
       61 ctgcaccctc agaggtgctg tgttgatgta aacggtactt ctgtagatat agaaattagt
      121 tttggttttc atgtttttac tgatgaaaaa caaaccggaa tgctgatgaa atttaaggag
      181 gaacagaggt ttttttgtag ggaacgctat gagggcagca aaactatcgt tcacagaata
      241 cttacagcga tagaaaacgg tgaatacatt acagcattta tttcaaaggg gcaggggcag
      301 cggtattacc atcttagcca tcatgatgac ttcattttga tggaaataag aaagcctcaa
      361 gatagaaata attctttgcg tattcatgtt gttacagctt acacgcttga tgaatggggg
      421 actgtaaata aaggacgtaa cctgcggttt agatatgtgc tggaacagcg actgcaggga
      481 aagaagattg tgtaaaaaac aaaaagcgcc taaggcgcct ttgttttttg cagaatttcg
      541 gtctggcctt tcgttatccc gctcacaggc tgggagggtg tgacccccgg catcagcacc
      601 cctctctcga ggttccggtt tgtgctgaca acattagtat cctattccac atgttcgttg
      661 tcaaactagc gtactttttg gtgttcattg gtgtttatag gttgtcattt accctctttg
      721 tggttataag tgtttatagg ttttcattgt tttttatagg tgttcatatg aagttgcttg
      781 atagtaatga agtgtgtgag ctcttaggca tcagtaagtc cactttgtat cgttggtgcg
      841 gggtgtctga ggatttttct ggcttgggtc taagtagcgg tcttcctcag gctaacgcta
      901 ctcagaactc tttaggcagg gaaaataggc tcgttaggag ggaattacag caaaacgctc
      961 tcggtgtcga agagacgcca agcgacttcc ctcgtccttt caagatcggt cgttcgttta
     1021 aatggaaaga cgccgaaatt atggcttggc ttgaaacgcg acgcgtttga ttgatagatc
     1081 ttcttgagat catttggatc tcgtcgtagt cttttgtcct gtaaacgaaa aaaccaccat
     1141 ggcaggtggt ttttcgaagg ttatttaatc ctggcagatt gaataaccgt ggtaacagcc
     1201 ttgtgcgaga cgtgtcacca aatctgtcct ttcagtgtag cctcactaag gccaccactt
     1261 caagaacttt gaatacatct ctcgcacatc ctgtttacca atggctaccg ccactggcga
     1321 tttttcgtgt ctgttccggg ttggactcaa gatgatagtt accgggacaa cgtggtagtc
     1381 gggctgaacg gggggttctt gcatacagcc cagcttggag cgaactgtct aaacggaacg
     1441 ggacgtggtg atttaggtaa agcttccacc acaacacgga tgccgcagga cgggaacagg
     1501 agagcgcaag agggagccgc cagggggaaa cgcctggtat ctttaagtcc tgtcgggttt
     1561 cgccacctct gacttgagcg tcgatttttg tgatgctcgt caggggggcg gagcctatgg
     1621 aaaaacgcca gcggcgtggc cttctctggg ttcttgtttt ttgctcacat gtttcttttg
     1681 gtgttatccc ctgattctgt ggataaccgc attaccgtct ttgagtgagc tgataccgct
     1741 cgccgcagcc gaacgaccga gcgtagcgag tcagtgagcg aggaagcgga agagcgtcgg
     1801 aagttgcatt ttctccttac acatctgtgc ggcatttcac acccggcatg gcgcactttt
     1861 catacaatcc gcactgatgc cgcatggtta agccagtata cactccgcta tcgctacgtg
     1921 actgggtcat ggctgcggcc tgacgcgccc tgacgggctt gtctgctccc ggcatccgct
     1981 cacagacaag ctgtgaccgt ctccgggagc tgtatgtgtc agaggttttc accgtcatcc
     2041 ccgaagcgtg cgaggcagct gcggtaaagc tcatcggcgt ggtcgtgaag cgattcacag
     2101 atgtctgcct gttcatccgc gtccagttcg ttgagctttt ccagcagcgt taatgtctgg
     2161 cttctgataa agcgggccat gttaagggcg gttttttcct gtttagtcac tgatgcctcc
     2221 gtgtaagggg ggatttctgt tcatggggta atgataccga tgaaacgcga gaggatgctc
     2281 acgatacggg ttactgatga tgaacatgca cggttactgg aacgctgtga gggtaaacag
     2341 ctggcggtat ggatgcggcg ggtctgtctg ggtgagccgg ttgcccgttc cgggaagctg
     2401 ccgacactgg caccgccgtt actgcgccag ctggctgcca tcgggaataa tctgaatcag
     2461 acggcgagga aggtgaacag cgggcagtgg tcttccggtg accgggttca ggtggtggcc
     2521 gcactgatgg ccatcgagag agagttgcgc agcttacggc aggtcgtcag ggaacatgga
     2581 gcgcgggatg atagttaagt ttcatgccag gggaaaaggc ggtggcagtg gtccggttga
     2641 ttacctgctg ggaagggagc gtaaccggga aggggcaacg gtgcttcagg gtaatccgga
     2701 agaagtccgg gaactcatcg atgccacgcc atttgcgaag aaatacacgt caggtgttct
     2761 gtcgttcgcg gagaaggagc tgccgcctgg agggcgtgaa aaagtgatgg cgagctttga
     2821 gcgtgtactg atgcccggtc tcgagaaaaa tcagtacagc atcctgtggg tggagcacca
     2881 ggacaaggga cggcttgagc tgaattttgt cattccgaac atggagctac agaccggaaa
     2941 acgcctccag ccgtactacg accgggcaga caggccgaga attgatgcct ggcagacgct
     3001 ggttaatcac cattacgggc tgcatgaccc caacgccccg gagaaccgcc ggacgctgac
     3061 ccttcctgat aacctgccgg aaacgaaaca ggcgcttgca gagagcgtca cacgcgggat
     3121 agacgctctt tatcatgtcg gggagataaa aggccgtcag gatgtgattc aggcgctcac
     3181 agaggcaggg cttgaagtgg tcagggtgac gcgaagcagt atcagcattg cagacccgaa
     3241 cggtgggaag aatatcaggc tgaaaggagc attttatgag caatctttta cagacgggcg
     3301 cggagttcga gaaaaagctg aaagagagag ccgaatctac agagacaatg ctgaacgacg
     3361 agttcagcaa gctcgaaaaa tctgtaagca aggctgtgac atcaaacgag acgaaaatca
     3421 aagacgctat agccctgttc acagcttcga cagaggaatc actgaaaaaa caccgggaag
     3481 gggtgaaaga ggcgatgatg cagcacagga aggacgtgtt aaagctggca gggaatacgg
     3541 gcatgatgtt actggggatg gtccttttcc tgtttaccgt gagtggcggg acgctctggt
     3601 atcttggcgg gcggatacag gcgaacctgg aagaaatcag gatacaggaa gaaacattgc
     3661 agaaactgaa cgcgaagaca tggggcgtgg agtttgtgca ggacgggaga aggaaatttc
     3721 tggtcatccc gcaggggaaa tcggcaacgg tgattcccta tcaggagaag gactgggtac
     3781 aactgacgga gtgacacaga gtgacggagc tggaaagaca tttgctgaac gccttagagc
     3841 aactgcaaca ggactatatg cagcggctga gcgaatggga gagcgccttc gtggaattgc
     3901 agaaaatgtt ttcgcttacg caacgggaca acgcgatgct gaacgagcag gtcatgcagt
     3961 tgagtcagca ggtgcagcac ttgagcgagc ggacagaacg cttgagccag ttatacagcg
     4021 agaacaggag ataagggacg aacggctgat acaggagcgc gaacatgagt tatccctgga
     4081 gcgtgagcgc cagctggaaa tacaggaacg gacactggat ggcatggtaa tcagagacag
     4141 gctaaaatgt tgtcagcgcg tttccggtgc attttttggg ataatggttg gttcgggggc
     4201 accgggaacg cgcttcagtc agaccttgct gaaaacacag gaacgcgtta aaacgcatac
     4261 gggcgcgatt ctggtgtgtc ttttgttgct gtgttttgcc tctattgcca gatcgcgctc
     4321 attcccctga acttctgttt tcccgctccg gtccccgtct tcttcgcttc cgaaagcatg
     4381 aaaaaaatcc gtttcagctg tctctggctg gcaattcctg cgtgattcac atggctgcat
     4441 agctatgcat gtggttaaaa tttaccgggt gcgatcgcgg cagtttttcg ggtggtttgt
     4501 tgccattttt acctgtctgc tgccgtgatc gcaccgaacg cgtttctgcg gtgcgggcaa
     4561 cggatgttat ggtaaatatt ggtgctctgg gatgaagcga aaataggctt tttttcgcta
     4621 ttttagcctg ttcaggaacg gcaagagtaa atatctggga gcatgaagct cgttaacctg
     4681 aatggagatc ctgatgatgg acaaagatac caccacccta aaacgcactt tggctcataa
     4741 tcgagccttt agcgataata ttaaccgcag tggcatagcc tggtgctata acactgagat
     4801 tgtactcgct gcttgtgagg cgattgaagc cgaactacaa cggcgaggat gtttgtaaca
     4861 ataagaaaac ccgcatcagc gggtttttta gtctctgaga cgcgctaccg ctaaattatt
     4921 tttctctcta tccgccctgg cttgccccct acaaccccat ggagcacaag gagcacaggg
     4981 agaaccatcg agcacaacga gcaccgcctt cctcttataa atcattatta atcatataat
     5041 taaacaactt cattgtaata tatattactt tttatgtttt taaatgtaat gtttattgcg
     5101 atttagcttg tttttaactc tattttttca gatgagaaca agctgccagc aatgaataac
     5161 tatttgattt tattggtttt ttcaataaat tagtgtccat agacaaacgg gagacgacta
     5221 tgtccgcaag agcaagaaaa gcaggtaaga gaaatcagtc agaacgacgt caggatttga
     5281 ttgaaaaatt gtgggaagac gacgaaatcg atacttggca tcgacttgaa aatgatgggt
     5341 actcaacagt tccacgttat ttgcctttga taggcgatct catggatggt ctgtcaaaag
     5401 gatcaccatt atcaacaacc tacttggctt tatggttcag ggtttctgat gaggggttga
     5461 ttgaaataag agataaagca gcactggctt ttgaatcagg gttcgctagt gaaagaggcg
     5521 taactacatg ggcagggaga atgaaaaagc taaaagaact ggggttcata tcctgtcgtg
     5581 aaggcagcac cggtgaattt cattacgtgt taattgttca cccattagtt gcagtcaaaa
     5641 agctgcttga tgaagggatt atccctaaag gaaagactta taacattttg tcggagcgtg
     5701 taattgaggt gggagcctct tgggagggtt aa
//
