LOCUS       NZ_CP053652             5279 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain CFS3246 plasmid pCFS3246-3, complete
            sequence.
ACCESSION   NZ_CP053652
VERSION     NZ_CP053652.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN08522703
            Assembly: GCF_009866925.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5279)
  AUTHORS   Nguyen,S.V., Hurley,D., Bai,L., Naithani,A., El Garch,F.,
            Woehrle,F., Miossec,C., Roques,B., Gaora,P.O., Bono,J.L. and
            Fanning,S.
  TITLE     Comparative genomics of Escherichia coli recovered from cattle
            presenting with diarrhoea or mastitis elaborating a variable geno-
            and phenotype under colistin selection
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5279)
  AUTHORS   Naithani,A., Nguyen,S.V., Fanning,S. and Bono,J.L.
  TITLE     Direct Submission
  JOURNAL   Submitted (14-MAY-2020) Centre for Food Safety, University College
            Dublin, UCD O'Brien Science Centre South, Dublin D04 V1W8, Ireland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Canu v. v. 1.6
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 30.0x
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 04:52:49
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,927
            CDSs (total)                      :: 4,803
            Genes (coding)                    :: 4,590
            CDSs (with protein)               :: 4,590
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 13
            Pseudo Genes (total)              :: 213
            CDSs (without protein)            :: 213
            Pseudo Genes (ambiguous residues) :: 0 of 213
            Pseudo Genes (frameshifted)       :: 69 of 213
            Pseudo Genes (incomplete)         :: 148 of 213
            Pseudo Genes (internal stop)      :: 42 of 213
            Pseudo Genes (multiple problems)  :: 46 of 213
            Pseudo Genes (short protein)      :: 4 of 213
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP053652.1.
            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..5279
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="CFS3246"
                     /isolation_source="Bovine adult"
                     /host="Bos taurus"
                     /db_xref="taxon:562"
                     /plasmid="pCFS3246-3"
                     /geo_loc_name="France"
                     /collection_date="2004-05-03"
     gene            187..1071
                     /locus_tag="C4962_RS24240"
                     /old_locus_tag="C4962_26560"
     CDS             187..1071
                     /locus_tag="C4962_RS24240"
                     /old_locus_tag="C4962_26560"
                     /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            1068..1469
                     /locus_tag="C4962_RS24245"
                     /old_locus_tag="C4962_26565"
     CDS             1068..1469
                     /locus_tag="C4962_RS24245"
                     /old_locus_tag="C4962_26565"
                     /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(2289..2522)
                     /locus_tag="C4962_RS24255"
                     /old_locus_tag="C4962_26575"
     CDS             complement(2289..2522)
                     /locus_tag="C4962_RS24255"
                     /old_locus_tag="C4962_26575"
                     /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(2529..3047)
                     /locus_tag="C4962_RS24260"
                     /old_locus_tag="C4962_26580"
     CDS             complement(2529..3047)
                     /locus_tag="C4962_RS24260"
                     /old_locus_tag="C4962_26580"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /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(<3085..3516)
                     /locus_tag="C4962_RS24655"
                     /pseudo=""
     CDS             complement(<3085..3516)
                     /locus_tag="C4962_RS24655"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /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(3725..4048)
                     /locus_tag="C4962_RS24270"
                     /old_locus_tag="C4962_26590"
     CDS             complement(3725..4048)
                     /locus_tag="C4962_RS24270"
                     /old_locus_tag="C4962_26590"
                     /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            4113..4304
                     /locus_tag="C4962_RS24275"
                     /old_locus_tag="C4962_26595"
     CDS             4113..4304
                     /locus_tag="C4962_RS24275"
                     /old_locus_tag="C4962_26595"
                     /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            4959..5090
                     /locus_tag="C4962_RS24280"
                     /old_locus_tag="C4962_26600"
     CDS             4959..5090
                     /locus_tag="C4962_RS24280"
                     /old_locus_tag="C4962_26600"
                     /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(4397..4480)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.07e-36"
     Typing          4491..5028
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.583"
                     /coverage="99.0"
                     /evalue="1.77e-167"
     Typing          complement(2186..3735)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.603"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gcggtcttgt acaccctgtt accacggttc agaagttccc caacttactg aaccctcgaa
       61 aaaaccgact ccccagtcgg tttttttcgt ttgatggcta agagtacgct gacgttatac
      121 tgaacgtcaa ggaaagcgtt gacgctgttc cctctaccaa aaaaaagaga tttgtaagga
      181 ataaaaatgg ctgtgacagt tgggtttatt agtgagaaag gtggggttgg taaaacaacg
      241 tcctgttatc acattgccga aggacttagt cgttttcatg aaaaacgtgt tttagttata
      301 gatgcagatt atcaacgcgg aggtataact ggaagatttt tccctaaact gatcgaaaac
      361 tttggaaatc aagcaccgca aggaacaacg ttatttaaca agtatcagca attatatagc
      421 gcggcacaac aaacgactga catagacata attaaattta atagtggtat cgatgtcatt
      481 ccagccgacc ctcgcttatc aaccgtttca actgataagc tacctagtac aaacaatata
      541 agatcgaaca atgccattct tttacagcat ttaaaaacca taagcgctgt attatcacct
      601 attgcagata attatgacta catattgatt gattcacacc ccgaagtttc tgatgtcatg
      661 cgctctataa tctacgcatc agattattgt gtatcaccgg taaaactaga caggcaatca
      721 tctattggtg tggccacggt cataggtgag ataaataatg taaatgaaga tattgaaatg
      781 ctaagaaagg cactgcaagt cggcgattca tataaggaca cagttttcgc cggagcaatg
      841 ggaatgatgg ccagagaata tgcagaagaa ctgaagcaaa cagagcaata tgaatacaac
      901 aggcttcggc aagcaggtga catcttcaag cactacataa cggaaggtga tgggctaaga
      961 gtagctgcag cagagcgcgt ttcagtgtat gatgtacaga taagtaacgc ttacaaacaa
     1021 gcgtcacagt ttaagaactt gacgattgag tttatgagga cttgtcgatg atagatatcc
     1081 aaaaactgat atcttggctt ggcgttgagg gagctaaagc tggcttggat aaaagtgaaa
     1141 tgactaatgc cgagctaatt gaatcctttg gtaatttact tccaaagaac ccaagcaaat
     1201 taaaacgctc cgatctcgtt gaggagatta ttttagcaac aaggagaatg acacataaat
     1261 cagttgaaga actgatggaa atgtcaaaag aagatctgta ttcatatttc cacgatcaga
     1321 aatatagcag aaaagaactt cttgatttgt tatatactct tgaaatcaga cctgggagct
     1381 cagcaaagaa aaatctaacc gagttcacaa taagtgagat aagtgatatt ggcatgtatc
     1441 gtcgcgtagc gaaagggaat catgcataaa taaaagccac ctgtgaggtg gctttttata
     1501 ggataaaaaa atgccattta atataggcga tatagtttac ttaaagtcag aatcaaaagc
     1561 gatgacggtc atcggatatg gatcgtctca aaataacggt tacatagatc tagctaattg
     1621 tgcttggcta gataaagaca accgctattg ccaaatacta ttcttgtttc aaacgatcga
     1681 aaaaagaatc agttaaaaac tggcttatct tcattgagca taccggacga acctatttac
     1741 cataacatcc gttgcccgca ccgcagaaac gcgttcggtg cgatcacggc agcagacagg
     1801 taaaaatggc aacaaaccac ccgaaaaact gccgcgatcg cacccggtaa attttaacca
     1861 catgcatagc tatgcagcca tgtgaatcac gcaggaattg ccagccagag acagctgaaa
     1921 cggatttttt tcatgctttc ggaagcgaag aagacgggga ccggagcggg aaaacagaag
     1981 ttcaggggaa tgagcgcgat ctggcaatag aggcaaaaca cagcaacaaa agacacacca
     2041 gaatcgcgcc cgtatgcgtt ttaacgcgtt cctgtgtttt cagcaaggtc tgactgaagc
     2101 gcgttcccgg tgcccccgaa ccaaccatta tcccaaaaaa tgcaccggaa acgcgctgac
     2161 aacattttag cctgtctctg attaccatcc aagcgaaggg ccatcctgtg tccattcctg
     2221 tatttccggc tggcgctcac gctccaggga taactcatgt tcgcgctcct gtatcagccg
     2281 ttcgtccctt atctcctgtt ctcgctgtat aactggctca agcgttctgt ccgctcgctc
     2341 aagtgctgca cctgctgact caactgcatg acctgctcgt tcagcatcgc gttgtcccgt
     2401 tgcgtaagcg aaaacatttt ctgcaattcc acgaaggcgc tctcccattc gctcagccgc
     2461 tgcatatagt cctgttgcag ttgctctaag gcgttcagca aatgtctttc cagctccgtc
     2521 actctgtgtc actccgtcag ttgtacccag tccttctcct gatagggaat caccgttgcc
     2581 gatttcccgt acggaaggac cagaaatttc cttctcccgt cctgcacaaa ctccacgccc
     2641 catgtcttcg cgttcagttt ctgcaatgtt tcttcctgta tcctgatttc ttccaggttc
     2701 gcctgtatcc gcccgccaag ataccagagc gtcccgccac tcacggtaaa caggaaaagg
     2761 accatcccca gtaacatcat gcccgtattc cctgccagct ttaacacgtc cttcctgtgc
     2821 tgcatcatcg cctctttcac cccttcccgg tgttttttca gtgattcctc tgtcgaagct
     2881 gtgaacaggg ctatagcgtc tttgattttc gtctcgtttg atgtcacagc cttgcttaca
     2941 gatttttcga gcttgctgaa ctcgtcgttc agcattgtct ctgtagattc ggctctctct
     3001 ttcagctttt tctcgaactc cgcgcccgtc tgtaaaagat tgctcataga atgctccttt
     3061 cagtctgata ttcttcccgc cgttcgggtc tgcaatgctg atactgcttc gcgtcaccct
     3121 gaccacttca agccctgcct ctgtgagcgc ctgaatcaca tcctgacggc cttttatctc
     3181 cccgacatga taaagagcgt ctatcccgcg tgtgacgctc tctgcaagcg cctgtttcgt
     3241 ttccggcagg ttatcaggga gagtcagtat ccggcggttc tccggggcgt tggggtcatg
     3301 cagcccgtaa tggtgattaa ccagcgtctg ccaggcatca attctcggcc tgtctgcccg
     3361 gtcgtagtac ggctggaggc gttttccgct ctgtagctcc atgttcggaa tgacaaaatt
     3421 cagctcaagc cgtcccttgt cctggtgctc cacccacagg atgctgtact gatttttttc
     3481 gagaccgggc atcagtacac gctcaaagct cgccatcacc ttttcacgtc ctcccggcgg
     3541 cagctccttc tccgcgaacg acagaacacc tgacgtgtat ttcttcgcaa atggcgtggc
     3601 atcgatgagt tcccggactt cttccggatt accctgaagc accgttgccc cttcccggtt
     3661 acgctccctt cccagcaggt aatcaaccgg accactgcca ccgccttttc ccctggcatg
     3721 aaacttaact atcatcccgc gctccatgtt ccctgacgac ctgccgtaag ctgcgcaact
     3781 ctctctcgat ggccatcagt gcggccacca cctgaacccg gtcaccggaa gaccactgcc
     3841 cgctgttcac cttcctcgcc gtctgattca gattattccc gatggcagcc agctggcgca
     3901 gtaacggcgg tgccagtgtc ggcagcttcc cggaacgggc aaccggctca cccagacaga
     3961 cccgccgcat ccataccgcc agctgtttac cctcacagcg ttccagtaac cgtgcatgtt
     4021 catcatcagt aacccgtatc gtgagcatcc tctcgcgttt catcggtatc attaccccat
     4081 gaacagaaat ccccccttac acggaggcat cagtgactaa acaggaaaaa accgccctta
     4141 acatggcccg ctttatcaga agccagacat taacgctgct ggaaaagctc aacgaactgg
     4201 acgcggatga acaggcagac atctgtgaat cgcttcacga ccacgccgat gagctttacc
     4261 gcagctgcct cgcacgcttc ggggatgacg gtgaaaacct ctgacacata cagctccagg
     4321 agacggtcac agcttgtctg tgagcggatg ccgggagcag acaagcccgt cagggcgcgt
     4381 caggccgttg accttgcggg tgtcggggcg cagccatgac ccagtcacgt agcgatagcg
     4441 gagtgtatac tggcttaacc atgcggcatc agtgcggatt gtatgaaaag tgcgccatgc
     4501 cgggtgtgaa atgccgcaca gatgtgtaag gagaaaatgc aacttccgac gctcttccgc
     4561 ttcctcgctc actgactcgc tacgctcggt cgttcggctg cggcgagcgg tatcagctca
     4621 ctcaaagacg gtaatgcggt tatccacaga atcaggggat aacaccaaaa gaaacatgtg
     4681 agcaaaaaac aagaacccag agaaggccac gccgctggcg tttttccata ggctccgccc
     4741 ccctgacgag catcacaaaa accgacgctc aagtcagagg tggcgaaacc cgacaggact
     4801 ataaagatac caggcgtttc cccctggtgg ctccctcgtg cgctctcctg ttcctgcctt
     4861 tcggtttacc ggtgtcattc cgctgttatg gccgcgttta tctcattcca cgcctgacac
     4921 tcagttccgg gtaggcagtt cgctccaagc tggactgtat gcacgaaccc cccgttcagt
     4981 ccgactgctg cgcctgttcc ggtaactatc gacttgagtc caacccggaa agacacgaca
     5041 aagcgccact ggcagcagcc atgagtaaag gggtgtacaa gatttactga gtgagagttc
     5101 ttgaagtatc agccttagag aggctaaact ggaataacag aatttggttt cagcggtctt
     5161 gtacaccctg ttaccacggt tcagaagttc cccaacttac tgaaccctcg aaaaaaagtg
     5221 agagttcttg aagtatcagc cttagagagg ctaaactgga ataacagaat ttggtttca
//
