LOCUS       NZ_CP122716             5125 bp    DNA     circular CON 08-JUN-2024
DEFINITION  Escherichia coli strain ETEC1749 plasmid unnamed4, complete
            sequence.
ACCESSION   NZ_CP122716
VERSION     NZ_CP122716.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN32549626
            Assembly: GCF_030013435.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5125)
  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 5125)
  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                   :: 408x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_030013435.1-RS_2024_06_08
            Annotation Date                   :: 06/08/2024 05:03:10
            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)                     :: 5,704
            CDSs (total)                      :: 5,579
            Genes (coding)                    :: 5,222
            CDSs (with protein)               :: 5,222
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 357
            CDSs (without protein)            :: 357
            Pseudo Genes (ambiguous residues) :: 0 of 357
            Pseudo Genes (frameshifted)       :: 160 of 357
            Pseudo Genes (incomplete)         :: 208 of 357
            Pseudo Genes (internal stop)      :: 73 of 357
            Pseudo Genes (multiple problems)  :: 74 of 357
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP122716.1.
            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..5125
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="ETEC1749"
                     /isolation_source="feces"
                     /host="Sus scrofa"
                     /db_xref="taxon:562"
                     /plasmid="unnamed4"
                     /geo_loc_name="Belgium"
                     /collection_date="2021"
                     /collected_by="IMM_DI04"
     gene            1..885
                     /locus_tag="QDX02_RS27450"
                     /old_locus_tag="QDX02_27450"
     CDS             1..885
                     /locus_tag="QDX02_RS27450"
                     /old_locus_tag="QDX02_27450"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505259.1"
                     /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_001505259.1"
                     /translation="MAVTVGFISEKGGVGKTTSCYHIAEGLSRFHEKRVLVIDADYQRG
                     GITGRFFPKLIENFGNQAPQGTTLFNKYQQLYSAAQQTTDIDIIKFNSGIDVIPADPRL
                     STVSTDKLPSTNNIRSNNAILLQHLKTISAVLSPIADNYDYILIDSHPEVSDVMRSIIY
                     ASDYCVSPVKLDRQSSIGVATVIGEINNVNEDIEMLRKALQVGDSYKDTVFAGAMGMMA
                     REYAEELKQTEQYEYNRLRQAGDIFKHYITEGDGLRVAAAERVSVYDVQISNAYKQASQ
                     FKNLTIEFMRTCR"
                     /name="ParA family protein"
     gene            882..1283
                     /locus_tag="QDX02_RS27455"
                     /old_locus_tag="QDX02_27455"
     CDS             882..1283
                     /locus_tag="QDX02_RS27455"
                     /old_locus_tag="QDX02_27455"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505260.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001505260.1"
                     /translation="MIDIQKLISWLGVEGAKAGLDKSEMTNAELIESFGNLLPKNPSKL
                     KRSDLVEEIILATRRMTHKSVEELMEMSKEDLYSYFHDQKYSRKELLDLLYTLEIRPGS
                     SAKKNLTEFTISEISDIGMYRRVAKGNHA"
                     /name="hypothetical protein"
     gene            complement(2103..2336)
                     /locus_tag="QDX02_RS27460"
                     /old_locus_tag="QDX02_27460"
     CDS             complement(2103..2336)
                     /locus_tag="QDX02_RS27460"
                     /old_locus_tag="QDX02_27460"
                     /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            complement(2343..2861)
                     /locus_tag="QDX02_RS27465"
                     /old_locus_tag="QDX02_27465"
     CDS             complement(2343..2861)
                     /locus_tag="QDX02_RS27465"
                     /old_locus_tag="QDX02_27465"
                     /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            complement(<2899..3561)
                     /locus_tag="QDX02_RS27470"
                     /old_locus_tag="QDX02_27470"
                     /pseudo=""
     CDS             complement(<2899..3561)
                     /locus_tag="QDX02_RS27470"
                     /old_locus_tag="QDX02_27470"
                     /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            complement(3539..3862)
                     /locus_tag="QDX02_RS27475"
                     /old_locus_tag="QDX02_27475"
     CDS             complement(3539..3862)
                     /locus_tag="QDX02_RS27475"
                     /old_locus_tag="QDX02_27475"
                     /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            3927..4118
                     /locus_tag="QDX02_RS27480"
                     /old_locus_tag="QDX02_27480"
     CDS             3927..4118
                     /locus_tag="QDX02_RS27480"
                     /old_locus_tag="QDX02_27480"
                     /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            4748..4879
                     /locus_tag="QDX02_RS27485"
                     /old_locus_tag="QDX02_27485"
     CDS             4748..4879
                     /locus_tag="QDX02_RS27485"
                     /old_locus_tag="QDX02_27485"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001505258.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001505258.1"
                     /translation="MHEPPVQSDCCACSGNYRLESNPERHDKAPLAAAMSKGVYKIY"
                     /name="hypothetical protein"
     Typing          complement(4214..4387)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.0"
                     /coverage="100.0"
                     /evalue="5.699999999999999e-63"
     Typing          4311..4896
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.554"
                     /coverage="97.0"
                     /evalue="0.0"
     Typing          complement(2000..3549)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.603"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atggctgtga cagttgggtt tattagtgag aaaggtgggg ttggtaaaac aacgtcctgt
       61 tatcacattg ccgaaggact tagtcgtttt catgaaaaac gtgttttagt tatagatgca
      121 gattatcaac gcgggggtat aactggaaga tttttcccta aactgatcga aaactttgga
      181 aatcaagcac cgcaaggaac aacgttattt aacaagtatc agcaattata tagcgcggca
      241 caacaaacga ctgacataga cataattaaa tttaatagtg gtatcgatgt cattccagcc
      301 gaccctcgct tatcaaccgt ttcaactgat aagctaccta gtacaaacaa tataagatcg
      361 aacaatgcca ttcttttaca gcatttaaaa accataagcg ctgtattatc acctattgca
      421 gataattatg actacatatt gattgattca caccccgaag tttctgatgt catgcgctct
      481 ataatctacg catcagatta ttgtgtatca ccggtaaaac tagacaggca atcatctatt
      541 ggtgtggcca cggtcatagg tgagataaat aatgtaaatg aagatattga aatgctaaga
      601 aaggcactgc aagtcggcga ttcatataag gacacagttt tcgccggagc aatgggaatg
      661 atggccagag aatatgcaga agaactgaag caaacagagc aatatgaata caacaggctt
      721 cggcaagcag gtgacatctt caagcactac ataacggaag gtgatgggct aagagtagct
      781 gcagcagagc gcgtttcagt gtatgatgta cagataagta acgcttacaa acaagcgtca
      841 cagtttaaga acttgacgat tgagtttatg aggacttgtc gatgatagat atccaaaaac
      901 tgatatcttg gcttggcgtt gagggagcta aagctggctt ggataaaagt gaaatgacta
      961 atgccgagct aattgaatcc tttggtaatt tacttccaaa gaacccaagc aaattaaaac
     1021 gctccgatct cgttgaggag attattttag caacaaggag aatgacacat aaatcagttg
     1081 aagaactgat ggaaatgtca aaagaagatc tgtattcata tttccacgat cagaaatata
     1141 gcagaaaaga acttcttgat ttgttatata ctcttgaaat cagacctggg agctcagcaa
     1201 agaaaaatct aaccgagttc acaataagtg agataagtga tattggcatg tatcgtcgcg
     1261 tagcgaaagg gaatcatgca taaataaaag ccacctgtga ggtggctttt tataggataa
     1321 aaaaatgcca tttaatatag gcgatatagt ttacttaaag tcagaatcaa aagcgatgac
     1381 ggtcatcgga tatggatcgt ctcaaaataa cggttacata gatctagcta attgtgcttg
     1441 gctagataaa gacaaccgct attgccaaat actattcttg tttcaaacga tcgaaaaaag
     1501 aatcagttaa aaactggctt atcttcattg agcataccgg acgaacctat ttaccataac
     1561 atccgttgcc cgcaccgcag aaacgcgttc ggtgcgatca cggcagcaga caggtaaaaa
     1621 tggcaacaaa ccacccgaaa aactgccgcg atcgcacccg gtaaatttta accacatgca
     1681 tagctatgca gccatgtgaa tcacgcagga attgccagcc agagacagct gaaacggatt
     1741 tttttcatgc tttcggaagc gaagaagacg gggaccggag cgggaaaaca gaagttcagg
     1801 ggaatgagcg cgatctggca atagaggcaa aacacagcaa caaaagacac accagaatcg
     1861 cgcccgtatg cgttttaacg cgttcctgtg ttttcagcaa ggtctgactg aagcgcgttc
     1921 ccggtgcccc cgaaccaacc attatcccaa aaaatgcacc ggaaacgcgc tgacaacatt
     1981 ttagcctgtc tctgattacc atccaagcga agggccatcc tgtgtccatt cctgtatttc
     2041 cggctggcgc tcacgctcca gggataactc atgttcgcgc tcctgtatca gccgttcgtc
     2101 ccttatctcc tgttctcgct gtataactgg ctcaagcgtt ctgtccgctc gctcaagtgc
     2161 tgcacctgct gactcaactg catgacctgc tcgttcagca tcgcgttgtc ccgttgcgta
     2221 agcgaaaaca ttttctgcaa ttccacgaag gcgctctccc attcgctcag ccgctgcata
     2281 tagtcctgtt gcagttgctc taaggcgttc agcaaatgtc tttccagctc cgtcactctg
     2341 tgtcactccg tcagttgtac ccagtccttc tcctgatagg gaatcaccgt tgccgatttc
     2401 ccgtacggaa ggaccagaaa tttccttctc ccgtcctgca caaactccac gccccatgtc
     2461 ttcgcgttca gtttctgcaa tgtttcttcc tgtatcctga tttcttccag gttcgcctgt
     2521 atccgcccgc caagatacca gagcgtcccg ccactcacgg taaacaggaa aaggaccatc
     2581 cccagtaaca tcatgcccgt attccctgcc agctttaaca cgtccttcct gtgctgcatc
     2641 atcgcctctt tcaccccttc ccggtgtttt ttcagtgatt cctctgtcga agctgtgaac
     2701 agggctatag cgtctttgat tttcgtctcg tttgatgtca cagccttgct tacagatttt
     2761 tcgagcttgc tgaactcgtc gttcagcatt gtctctgtag attcggctct ctctttcagc
     2821 tttttctcga actccgcgcc cgtctgtaaa agattgctca tagaatgctc ctttcagtct
     2881 gatattcttc ccgccgttcg ggtctgcaat gctgatactg cttcgcgtca ccctgaccac
     2941 ttcaagccct gcctctgtga gcgcctgaat cacatcctga cggcctttta tctccccgac
     3001 atgataaaga gcgtctatcc cgcgtgtgac gctctctgca agcgcctgtt tcgtttccgg
     3061 caggttatca gggagagtca gtatccggcg gttctccggg gcgttggggt catgcagccc
     3121 gtaatggtga ttaaccagcg tctgccaggc atcaattctc ggcctgtctg cccggtcgta
     3181 gtacggctgg aggcgttttc cgctctgtag ctccatgttc ggaatgacaa aattcagctc
     3241 aagccgtccc ttgtcctggt gctccaccca caggatgctg tactgatttt tttcgagacc
     3301 gggcatcagt acacgctcaa agctcgccat caccttttca cgtcctcccg gcggcagctc
     3361 cttctccgcg aacgacagaa cacctgacgt gtatttcttc gcaaatggcg tggcatcgat
     3421 gagttcccgg acttcttccg gattaccctg aagcaccgtt gccccttccc ggttacgctc
     3481 ccttcccagc aggtaatcaa ccggaccact gccaccgcct tttcccctgg catgaaactt
     3541 aactatcatc ccgcgctcca tgttccctga cgacctgccg taagctgcgc aactctctct
     3601 cgatggccat cagtgcggcc accacctgaa cccggtcacc ggaagaccac tgcccgctgt
     3661 tcaccttcct cgccgtctga ttcagattat tcccgatggc agccagctgg cgcagtaacg
     3721 gcggtgccag tgtcggcagc ttcccggaac gggcaaccgg ctcacccaga cagacccgcc
     3781 gcatccatac cgccagctgt ttaccctcac agcgttccag taaccgtgca tgttcatcat
     3841 cagtaacccg tatcgtgagc atcctctcgc gtttcatcgg tatcattacc ccatgaacag
     3901 aaatcccccc ttacacggag gcatcagtga ctaaacagga aaaaaccgcc cttaacatgg
     3961 cccgctttat cagaagccag acattaacgc tgctggaaaa gctcaacgaa ctggacgcgg
     4021 atgaacaggc agacatctgt gaatcgcttc acgaccacgc cgatgagctt taccgcagct
     4081 gcctcgcacg cttcggggat gacggtgaaa acctctgaca catacagctc ccggagacgg
     4141 tcacagcttg tctgtgagcg gatgccggga gcagacaagc ccgtcagggc gcgtcaggcc
     4201 gttgaccttg cgggtgtcgg ggcgcagcca tgacccagtc acgtagcgat agcggagtgt
     4261 atactgactt actatgttgg catgagtgcg ggtatcagga aagtgcttca tgtggcagga
     4321 gaaaaaaggc ggcaccggag cgtcagcaga atatgtgata caggatatat tccgcttcct
     4381 cgctcactga ctcgctacgc tcggtcgttc gactgcggcg agcggaaatg gcttacgaac
     4441 ggggcggaga tttcctggaa gatgccagga agatacttaa cagggaagcg atagggtcgc
     4501 ggcgaagccg tttttccata ggctccgccc cctgacaagc atcacgaaat ctgacgctca
     4561 aatcagtggt ggcgaaaccc gacaggacta taaagatacc aggcgtttcc ccctggtggc
     4621 tccctcgtgc gctctcctgt tcctgccttt cggtttaccg gtgtcattcc gctgttatgg
     4681 ccgcgtttat ctcattccac gcctgacact cagttccggg taggcagttc gctccaagct
     4741 ggactgtatg cacgaacccc ccgttcagtc cgactgctgc gcctgttccg gtaactatcg
     4801 acttgagtcc aacccggaaa gacacgacaa agcgccactg gcagcagcca tgagtaaagg
     4861 ggtgtacaag atttactgag tgagagttct tgaagtatca gccttagaga ggctaaactg
     4921 gaataacaga atttggtttc agcggtcttg tacaccctgt taccacggtt cagaagttcc
     4981 ccaacttact gaaccctcga aaaaaccgac tccccagtcg gttttttcgt ttgatggcta
     5041 agagtacgct gacgttatac tgaacgtcaa ggaaagcgtt gacgctgttc cctctaccaa
     5101 aaaaagagat ttgtaaggaa taaaa
//
