LOCUS       NZ_CP122863             5062 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC1720 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP122863
VERSION     NZ_CP122863.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32549599
            Assembly: GCF_030013865.1
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                   :: 376x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030013865.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 05:22:55
            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)                     :: 5,235
            CDSs (total)                      :: 5,114
            Genes (coding)                    :: 4,754
            CDSs (with protein)               :: 4,754
            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)              :: 360
            CDSs (without protein)            :: 360
            Pseudo Genes (ambiguous residues) :: 0 of 360
            Pseudo Genes (frameshifted)       :: 114 of 360
            Pseudo Genes (incomplete)         :: 253 of 360
            Pseudo Genes (internal stop)      :: 49 of 360
            Pseudo Genes (multiple problems)  :: 51 of 360
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122863.1.
            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="ETEC1720"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed4"
                     /geo_loc_name="Belgium"
                     /collection_date="2020"
                     /collected_by="IMM_DI04"
     gene            join(4750..5062,1..11)
                     /locus_tag="QDY31_RS24090"
                     /old_locus_tag="QDY31_24090"
     CDS             join(4750..5062,1..11)
                     /locus_tag="QDY31_RS24090"
                     /old_locus_tag="QDY31_24090"
                     /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"
     gene            220..>651
                     /locus_tag="QDY31_RS24095"
                     /old_locus_tag="QDY31_24095"
                     /pseudo=""
     CDS             220..>651
                     /locus_tag="QDY31_RS24095"
                     /old_locus_tag="QDY31_24095"
                     /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="QDY31_RS24100"
                     /old_locus_tag="QDY31_24100"
     CDS             689..1207
                     /locus_tag="QDY31_RS24100"
                     /old_locus_tag="QDY31_24100"
                     /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            1214..1447
                     /locus_tag="QDY31_RS24105"
                     /old_locus_tag="QDY31_24105"
     CDS             1214..1447
                     /locus_tag="QDY31_RS24105"
                     /old_locus_tag="QDY31_24105"
                     /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            1478..1639
                     /locus_tag="QDY31_RS26175"
     CDS             1478..1639
                     /locus_tag="QDY31_RS26175"
                     /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            1805..1990
                     /locus_tag="QDY31_RS24110"
                     /old_locus_tag="QDY31_24110"
     CDS             1805..1990
                     /locus_tag="QDY31_RS24110"
                     /old_locus_tag="QDY31_24110"
                     /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            1980..2234
                     /locus_tag="QDY31_RS24115"
                     /old_locus_tag="QDY31_24115"
     CDS             1980..2234
                     /locus_tag="QDY31_RS24115"
                     /old_locus_tag="QDY31_24115"
                     /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(2265..3323)
                     /locus_tag="QDY31_RS24120"
                     /old_locus_tag="QDY31_24120"
     CDS             complement(2265..3323)
                     /locus_tag="QDY31_RS24120"
                     /old_locus_tag="QDY31_24120"
                     /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(3688..3819)
                     /locus_tag="QDY31_RS26180"
     CDS             complement(3688..3819)
                     /locus_tag="QDY31_RS26180"
                     /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            4120..4338
                     /locus_tag="QDY31_RS24125"
                     /old_locus_tag="QDY31_24125"
     CDS             4120..4338
                     /locus_tag="QDY31_RS24125"
                     /old_locus_tag="QDY31_24125"
                     /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            complement(4493..4684)
                     /locus_tag="QDY31_RS24130"
                     /old_locus_tag="QDY31_24130"
     CDS             complement(4493..4684)
                     /locus_tag="QDY31_RS24130"
                     /old_locus_tag="QDY31_24130"
                     /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"
     Typing          4318..4399
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          complement(3748..4294)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="97.814"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          2..1551
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.412"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4718..5052
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.75"
                     /coverage="95.0"
                     /evalue="1.95e-61"
ORIGIN
        1 atgatagtta agtttcatgc caggggaaaa ggtggtggca gtggtccggt tgattacctg
       61 ctgggaaggg agcgaaaccg ggaaggggca acggtgcttc agggtaatcc ggaagaagtc
      121 cgggaactca tcgatgccac gccatttgcg aagaaataca cgtccggtgt tctgtcgttc
      181 gcggagaatg agctgccgcc gggagaacgt gaaaaagtga tggcgagctt tgagtgtgta
      241 ctgatgcccg gtctcgaaaa aaatcagtac agcatcctgt gggtggagca ccaggacaag
      301 ggacggcttg agctgaattt tgtcattccg aacatggagc tacagaccgg aaaacgcctc
      361 cagccgtact acgaccgcgc agacaggcct agaattgatg cctggcagac gctggttaat
      421 caccattacg ggctgcatga cccgaacgcc ccggagaacc gcaggacgct gacactccct
      481 gataatctgc cggaaacgaa acaggcgctt gcagagagcg tcacacgcgg gatagacgct
      541 ctttatcatg tcggggagat aaaaggccgt caggatgtga ttcaggcgct cacagaggca
      601 gggcttgaag tggtcagggt gacgcgaagc agtatcagca ttgcagaccc gaacggcggg
      661 aagaatatca ggctgaaagg agcattttat gagcaatctt ttacagacgg gcgcggagtt
      721 cgagaaaaag ctgaaagaga gagccgaatc tacagagaca atgctgaacg acgagttcag
      781 caagctcgaa aaatctgtaa gcaaggctgt gacctcaaac gagacgaaaa tcaaagacgc
      841 tatagccctg ttcacaacgt cgacagagga atcgctggaa aaacaccggg aaggggtgaa
      901 agaggcgatg atgcagcaca ggaaggacgt gttaaagctg gcagggaata cgggcatgag
      961 gttgctgggg atagtctttc tcctgtttac cgcgagtggc gggacgctct ggtatcttgg
     1021 cgggcggata caggcgaacc tggaagaaat caggatacag gaagaaacat tgcagaaact
     1081 gaacgcgaag acatggggcg tggagtttgt gcaggacggg agaaggaaat ttctggtcct
     1141 tccgtacggg aaatcggcaa cggtgattcc ctatcagggg aaggactggg tacaactgac
     1201 ggagtgacac agagtgacgg agctggaaag acatttgctg aacgcattag agcaactgca
     1261 acaggactat atgcagcggc tgagcgaatg ggagagcgcc ttcgtggaat tgcagaaaat
     1321 gttttcgctt acgcaacggg acaacgcgat gctgaacgag caggtcatgc agttgagtca
     1381 gcaggtgcag cacttgagcg agcggacaga acgcttgagc ctgttataca gcgagaacag
     1441 gagataaggg acgaacggct gatacaggag cgcgaacatg cgttatccct ggagcgtgag
     1501 cgtcagccgg aaatacagga acgcacgctg gatggccctt cgctgggatg gtgaaacaat
     1561 gaaaaatggc agcttcagtg tattaagagg gggtaatgtg gcctgtacca tctggttgca
     1621 taggtattca tacggttaaa atttatcagg cgcgatcgcg gcagtttttc gggtggtttg
     1681 ttgccatttt tacctgtctg ctgccgtgat cgcgatgaac gcattttagc ggtgcgtaca
     1741 aggggtgtta tgttcaattc tccagcgtat attgggctgt ttacagcaat aggtgtaatg
     1801 ttctatgact gaagataacg ttaagaatat tagcgactac agaaagaata atgatgctgt
     1861 tgatgctaat agtagtgcta tttcaggtaa aagcgctcca gctaagctga gtgagaaact
     1921 tagaaataca gttccttctg gactgagggc ccaaatgcgc caacaaatga ggaataaaca
     1981 tggattctaa taacagtcag aaaaaccttc aagataagca tgctgatctt ctggataaaa
     2041 cttatactct cggctggttg gatgggtatt cagaagggta tgatgatgcc attgaagatt
     2101 gtcaaaatgc cttgaataaa ctggaaaatg aaaacgaatt gctcaatgaa attattgaaa
     2161 acaaagataa tgtaatcagt gaaatggcat ctagtgtggg cagggcgttg caaacggtaa
     2221 agaaaaataa ataaaaaaca ggcccttgaa aaagggcctg ttttttactc aatcataccg
     2281 gcaagagcga caatgttggg cacttgctta tcaagctgtg tctgatttac ctttattgtt
     2341 cttcccgcaa cattcttatt tcctgcggtt agtgtggcaa ttggaatacc aagtgctcct
     2401 gatacgacag atgctgtatt ggcatcattt acttcatact ggaacatgtt cctaaaggat
     2461 tttttattat tcggcgttga gcttccattt ggatgaatgc agaataaact tggttttgtt
     2521 tgccacactt tccaaatctc atcgccgatc tctgttacca cagttttgaa tgcgctagct
     2581 gatgagttgt tcatttgagt taatctgttt ccaacataca tgtatatttg tggtaatgac
     2641 atagaataac gattgctgtt taaatagaaa tctgactgtg gttcgttcag atgacgtcgc
     2701 tcgccataaa ctaaagaaag aactgcttta acagctcttt ttgatgaacc atcagcagag
     2761 aatggaatta ataggcgttc agctgcggtt aatgctaact cggtataaat agagaagctg
     2821 ggattacagt cgatgaaaac gcagctgtcg ccattatccc atgagttaca aatgtcacta
     2881 attagatcgt taatccaaag atgaacagtt ctccatgcgt catgaggtcc agggaatgat
     2941 gctccaacaa ctcttgatgc ttgaagttct aattgctcat cgccagtaac aagatataga
     3001 ttatctggga ttctgctatt gtatgtagat acgttgatta cgtagttaga acctgtattt
     3061 gtcggaatat atggacttct gatcctatcc tcaatatatc cagaaatagt ctttctttgt
     3121 gttgcagaat gaatctgatt tagcgtattt tcgccattaa ccatcccgcc aagtaacatt
     3181 gaggatgagt tagcttgtgg gcatagatca atcaccagaa ccttttttgt cgggttctgt
     3241 ctggcgtact cagaggctag ttgaaaggta agataacttt tccccactcc gcctttgtta
     3301 ttccatacgg catagatcgc catctatcac tcctaatata gttttgttgt tagctttaag
     3361 tcagagtact agagattatt gttctactgt tagtttcttt cagctaactg actgtgtttc
     3421 gagcggtatg gttagatgag ggtgtccgta ttggcatgac ctcttcagca tagtaggaac
     3481 gtgattgaaa ggatttcttg agatccttat tcgtgggatg taatcttctg cactgtaaac
     3541 gaaaaaacca cctggggagg tggtttttcg aaggatcagt aagttgggga acttctgaac
     3601 cgtggtaaca gggtgtacaa gaccactgcc accaaatctg tcctttcagt ttagctgtag
     3661 ttaggcttca acttcaagaa ctctgcgtta gtaatatctt gtacatccct taccagtggc
     3721 tgctgccagt ggcgttaagt cgtgtcttac cgggttggac tcaagacgat agttaccgga
     3781 taaggcgcag cggtcgggct gaacgggggg ttcgtgcaca cagcccagct tggagcgaac
     3841 gacctacacc gaactgagat accaacagcg tgagctatga gaaagcgcca cgcttcccga
     3901 agggagaaag gcggacaggt atccggtaag cggcagggtc ggaacaggag agcgcacgag
     3961 ggagcttcca gggggaaacg cctggtatct ttatagtcct gtcgggtttc gccacctctg
     4021 acttgagcgt cggtttttgt gatgctcgtc aggggggcgg agcctatgga aaaacgccat
     4081 ctacgcggct tttctctagc ccttcgtctt tttgctcaca tgtttctttt ggcgttatcc
     4141 cctgattctg tggataaccg tattaccgct tttgagtgcg cagacaccgc tcgccgcagc
     4201 cgaacgaccg agcgcagcga gtcagtgagc gaggaagcgg aagagcgtcg gaagttgcat
     4261 tttctcctta cgcatctgtg cggcatttca cacccggcat ggcgcacttt ccatacaatc
     4321 cgcactgatg ccacatagtt aagccagtat acactccgct atcgctacgt gactgggtca
     4381 tggctgcgcc ccgacacccg caaggtcaac ggcctgacgc gccctgacgg gcttgtctgc
     4441 tcccggcatc cgctcacagg caagctgtga ccgtctccgg gagctgtgtg tgtcagaggt
     4501 tttcaccgtc atccccgaag cgtgcgaggc aactgcggta aagttcatcg gcgtggtcgt
     4561 gaagcgattc acagatgtct gcctgttcat ccgcgtccag ttcgttgagc ttctccagca
     4621 gcgttaatgt ctggcttctg ataaagcggg ccatgttaag ggcggttttt tcctgtttag
     4681 tcactgatgc ctccgtgtaa ggggggattt ctgttcatgg gggtaatgat accgatgaaa
     4741 cgcgagagga tgctcacgat acgggttact gatgatgaac atgcacggtt actggaacgc
     4801 tgtgagggta aacagctggc ggtatggatg cggcgggtct gcctgggtga gccggttgcc
     4861 cgttccggga agctgccgac actggcaccg ccgttactgc gtcagctggc cgccatcggg
     4921 aataacctga atcagactgc gaggaaggtg aacagcgggc agtggtcttc cggtgaccgg
     4981 gttcaggtgg tggccgcact gatggccatc gagagagagt tgcgcagctt acggcaggtg
     5041 gtcagggaac agagagtgca gg
//
