LOCUS       NZ_CP122630             4568 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC4088 plasmid unnamed1, complete
            sequence.
ACCESSION   NZ_CP122630
VERSION     NZ_CP122630.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32549664
            Assembly: GCF_030013145.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4568)
  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 4568)
  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                   :: 229x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030013145.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 04:59:52
            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)                     :: 5,120
            CDSs (total)                      :: 5,000
            Genes (coding)                    :: 4,768
            CDSs (with protein)               :: 4,768
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 232
            CDSs (without protein)            :: 232
            Pseudo Genes (ambiguous residues) :: 0 of 232
            Pseudo Genes (frameshifted)       :: 97 of 232
            Pseudo Genes (incomplete)         :: 149 of 232
            Pseudo Genes (internal stop)      :: 47 of 232
            Pseudo Genes (multiple problems)  :: 53 of 232
            Pseudo Genes (short protein)      :: 1 of 232
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122630.1.
            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..4568
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC4088"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed1"
                     /geo_loc_name="Belgium"
                     /collection_date="2012"
                     /collected_by="IMM_DI04"
     gene            join(4256..4568,1..11)
                     /locus_tag="QDW58_RS24140"
                     /old_locus_tag="QDW58_24140"
     CDS             join(4256..4568,1..11)
                     /locus_tag="QDW58_RS24140"
                     /old_locus_tag="QDW58_24140"
                     /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_000956000.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGTR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            220..>651
                     /locus_tag="QDW58_RS24145"
                     /old_locus_tag="QDW58_24145"
                     /pseudo=""
     CDS             220..>651
                     /locus_tag="QDW58_RS24145"
                     /old_locus_tag="QDW58_24145"
                     /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="QDW58_RS24150"
                     /old_locus_tag="QDW58_24150"
     CDS             689..1207
                     /locus_tag="QDW58_RS24150"
                     /old_locus_tag="QDW58_24150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001525988.1"
                     /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_072650569.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNNEFRRLGESVSEAVTSNE
                     TKIRDAIALFTASTEESLEKHREGVKEAMMQHRRDVLKLAGNTGMMLLGIVFLLFTVSG
                     GTLWYLGGRIQANLEDIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVISFQ
                     GKEWVHLKG"
                     /name="MbeB family mobilization protein"
     gene            1214..1447
                     /locus_tag="QDW58_RS24155"
                     /old_locus_tag="QDW58_24155"
     CDS             1214..1447
                     /locus_tag="QDW58_RS24155"
                     /old_locus_tag="QDW58_24155"
                     /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            1811..2047
                     /locus_tag="QDW58_RS24160"
                     /old_locus_tag="QDW58_24160"
     CDS             1811..2047
                     /locus_tag="QDW58_RS24160"
                     /old_locus_tag="QDW58_24160"
                     /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_125075503.1"
                     /translation="MSIIIDREKYTALMTLIQTSQGYVGSKVQPNGYTLKCSFDTGFAC
                     CISRNTRNSNLSVHFENESTDPATHFAILSAIS"
                     /name="hypothetical protein"
     gene            complement(2169..2993)
                     /locus_tag="QDW58_RS24165"
                     /old_locus_tag="QDW58_24165"
     CDS             complement(2169..2993)
                     /locus_tag="QDW58_RS24165"
                     /old_locus_tag="QDW58_24165"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001423320.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NYN domain-containing protein"
                     /protein_id="WP_282834334.1"
                     /translation="MLVQTCGVPQAKKQPPCGVPQAKKQPSCGEPQANTPPTACRRKKT
                     ADAVFFISKMELTPLKTIVYVDGFNFYYRKLKDSNKKWLNIKAMVEKLLPDDEIIGINY
                     YTARISGRIDSDAPRRQQIYFNALKSIDNLSIHYGTFSVNESRMFLVQPLDFKHHLKNP
                     NQKIKFANVLKTEEKGSDVNLGCHLVRDGFQGKYEKAVIITNDTDLAEPMRVVKSELSL
                     YIELLSPVNKPARTLSAICDKVTLISDQSIADSQFEDVIVVGEKTVTKPAQW"
                     /name="NYN domain-containing protein"
     gene            complement(4000..4191)
                     /locus_tag="QDW58_RS24170"
                     /old_locus_tag="QDW58_24170"
     CDS             complement(4000..4191)
                     /locus_tag="QDW58_RS24170"
                     /old_locus_tag="QDW58_24170"
                     /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          3830..3915
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.851"
                     /coverage="100.0"
                     /evalue="3.99e-36"
     Typing          complement(3226..3752)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.025"
                     /coverage="90.0"
                     /evalue="1.52e-158"
     Typing          2..1551
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.42"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          4224..4567
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.261"
                     /coverage="97.0"
                     /evalue="1.3599999999999999e-67"
ORIGIN
        1 atgatagtta agtttcatgc caggggaaaa ggcggtggca gtggtccggt tgattacctg
       61 ctggggaggg agcgtaaccg ggagggcgca aaggtgcttc agggtaaccc ggaagaagtc
      121 cgggaactca tcgatgccac gccatttgcg aagaaataca cgtccggtgt tctgtcgttc
      181 gcggagaagg aactgccgcc gggaggacgt gaaaaagtga tggcgagttt tgagcgtgta
      241 ctgatgcccg gtctcgaaaa aaatcagtac agcattctgt gggtggagca ccaggacaag
      301 gggcggcttg agcttaattt tgtcattccg aacatggagc tacagagcgg aaaacgcctc
      361 cagccgtact acgaccgcgc agacaggccg agaattgatg cctggcagac gctggtgaat
      421 caccattacg ggctgcatga ccccaacgcc ccggagaacc gccggatact gactctccct
      481 gataacctgc cggaaacgaa acaggcgctt gcagagagcg tcacacgcgg gatagacgct
      541 ctttatcatg tcggggagat aaaaggccgt caggatgtga ttcaggcgct cacagaggca
      601 gggcttgaag tggtcagggt gacgcgaagc agtatcagca ttgcagaccc gaacggtggg
      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 atctctggaa aaacaccggg aaggggtgaa
      901 agaggcgatg atgcagcaca ggagggacgt gttaaagctg gcagggaata cgggcatgat
      961 gttgctgggg atagtctttc tcctgtttac cgtgagtggc gggacgctct ggtatcttgg
     1021 cgggaggata caggcgaacc tggaagatat caggaagcag gaagagacat tgcagaaact
     1081 gaacgcgaag acatggggcg tggagtttgt gcaggacggg aacaggaaat ttctggtcct
     1141 tccttacggg aagtcagcag aggtgatttc ctttcagggg aaggaatggg tacatctgaa
     1201 ggggtgacac 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 aggaacggtt gatacaggag cgcgaatatg cgttatccct ggaacgggag
     1501 cgtcagccgg aaatacagga acgcacgctg gatggccctt cgctgggatg gtgaaactat
     1561 gaaaaatggc aggttcagtg gattttgacg gactaatgta gtctgcacca tcttgttgca
     1621 taggtattca tgcggttaaa atttatcagg cgcgatcgcg gcagtttttc gggaggtttg
     1681 ttgcctgttt ttccggtttc ccgtcagaaa cgcgctgaga gcgtctgagg cggtgcgggc
     1741 aacgggagtt atggtaaata gatttattgc tgaggtttaa tgcctgcaga gtaatactaa
     1801 tggggatgtg atgagtatta ttattgatcg tgaaaaatat actgctttga tgacgttgat
     1861 ccagacatct caaggatatg ttggctcaaa agtacaacca aatggatata cattgaagtg
     1921 ttctttcgac actggttttg catgttgtat ctctagaaat actagaaata gtaacttatc
     1981 tgttcatttt gaaaatgaaa gtacagatcc tgcaactcac tttgctattt taagtgctat
     2041 tagctaattt tttattttct gcacatagct atagatttca tactctttat atttgcctga
     2101 aggtataatg caaaacataa aaagcccggg ggacgggctt ttttttcaac agaacgagta
     2161 tgtagccact accactgtgc tggttttgtc acggttttct caccaactac aataacgtct
     2221 tcaaactggc tatcagctat tgattggtcg cttataagag tgaccttatc gcatattgcg
     2281 ctcagggttc ttgctggttt gtttacagga gaaagtagtt caatataaag gctgagctct
     2341 gatttgacta ctctcattgg ttcagccaaa tctgtatcat tagttattat tacagccttc
     2401 tcgtatttcc cttggaaacc atctctaacc aagtggcaac ctaaattaac gtcagaaccc
     2461 ttttcttctg tctttaagac gtttgcaaac tttatttttt gattcgggtt ttttaagtga
     2521 tgtttgaaat caagaggctg cactaaaaac attctgcttt cattcaccga aaaagtacca
     2581 taatggatac ttaggttatc tatgcttttc agtgcattga aatatatttg ttgcctacga
     2641 ggtgcgtcag aatcaatcct tcctgagatc ctagccgtgt aatagttaat tcctattatt
     2701 tcatcatccg gtagcaattt ttcgaccatt gcttttatgt tcagccactt tttgttggaa
     2761 tctttcagct tacgataata aaagttaaag ccatcaacat aaactattgt tttcaatggg
     2821 gttagctcca ttttagatat aaaaaaaacc gcatctgcgg tttttttcct acggcacgcc
     2881 gtaggagggg tgtttgcctg cggctcgcca caggagggtt gtttcttcgc ctgcggcacg
     2941 ccacaggggg gttgtttctt cgcctgcggc acgccacagg tctgtaccaa cattattgca
     3001 ttttttttgt ctagtgcaaa tgttttatat ggtgacgaag taagccctac ctaaaggaga
     3061 aaagatcttc ttgagatcct ttttttctgc gcgtaatctc ctgctttgaa aacgaaaaaa
     3121 ccaccctggc aggtggtttt tcgaaggtta gttaatcctg gcagattctc taaccgcggt
     3181 aacggtcttg tgcgagacat gtcaccaaat ctgtcctttc agtgtagccg tagtcaggcc
     3241 gccacttcaa gaactctcga tacatctctc gcacatcctg tttaccagtg gccgttgcca
     3301 atggcgatta gtcgtgtctt tccgggttgg actcaagttg atagttaccg gataagacgc
     3361 agcggtcgga ctgaacgggg ggttcgtgca tacagtccag cttggagcga actgccttcc
     3421 cggagccgag tgtcaggcgt ggaatgagaa accgcggcca taacagcgga atgacaccgg
     3481 tacaccgaaa ggcaggaaca ggagagcgca cgagggagct tccaggggga aacgcctggt
     3541 atctttatag tcctgtcggg tttcgccacc tctgacttga gcgtcaattt ttgtgatgct
     3601 cgtcaggggg gcggagccta tggaaaaacg cctgcggcgc ggccttatcc cctgattctg
     3661 tggataaccg cattaccgtc tttgcgtgag ctgataccgc tcgccgcagc cgaacgaccg
     3721 agcgtagcga gtcagtgagc gaggaagcgg aagagcgcct gatgcggtat tttctcctta
     3781 cgcatctgtg cggtatttca caccgcatat ggtgctcttt tcttataatc tgcactgatg
     3841 ccacatagtt aagccagtat acactccgct atcgctacgt gactgggtca tggctgcgcc
     3901 ccgacacccg ctaaaacccc ctgacgcgcc ctgacgggct tgtctgctcc cggcatccgc
     3961 tcacagacaa gctgtgaccg tctccgggag ctgtatgtgt cagaggtttt caccgtcatc
     4021 cccgaagcgt gcgaggcagc tgcggtaaag ctcgtcggcg tggtcgtgaa gtgattcaca
     4081 aatatcggcc tgttcatctg cgtccagttc gttgagcttc tccagcagcg ttaatgtctg
     4141 gcttcttata aagcgggcca tgttaagggc ggttttttcc tgtttggtca ctgatgcctc
     4201 cgtgtaaggg ggatttctgt tcatgggggt aatgataccg atgaaacgcg agaggatgct
     4261 cacgatacgg gttactgatg atgaacatgc ccggttactt gaacgctgtg agggtaaaca
     4321 actggcggta tggatgcggc gggtctgcct gggggagccg gttgcccgtt ccgggaaact
     4381 gccgacactg gcaccgccgt tactgcgtca gctggccgcc atcgggaata acctgaatca
     4441 gacagcgagg aaggtgaaca gcgggcagtg gtcttccggt gaccgggttc aggtggtggc
     4501 cgcactgatg gccatcgggg atgagctgcg ccggctgcgt ctggccgtca gggaacaggg
     4561 gacgcggg
//
