LOCUS       NZ_CP053653             6648 bp    DNA     circular CON 16-JUN-2023
DEFINITION  Escherichia coli strain CFS3273 plasmid pCFS3273-3, complete
            sequence.
ACCESSION   NZ_CP053653
VERSION     NZ_CP053653.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN08522730
            Assembly: GCF_009866945.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6648)
  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  JOURNAL   Unpublished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 6648)
  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 05:09:57
            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)                     :: 5,436
            CDSs (total)                      :: 5,315
            Genes (coding)                    :: 5,011
            CDSs (with protein)               :: 5,011
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 304
            CDSs (without protein)            :: 304
            Pseudo Genes (ambiguous residues) :: 0 of 304
            Pseudo Genes (frameshifted)       :: 111 of 304
            Pseudo Genes (incomplete)         :: 204 of 304
            Pseudo Genes (internal stop)      :: 60 of 304
            Pseudo Genes (multiple problems)  :: 65 of 304
            Pseudo Genes (short protein)      :: 4 of 304
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP053653.1.
            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..6648
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="CFS3273"
                     /isolation_source="Bovine adult"
                     /host="Bos taurus"
                     /db_xref="taxon:562"
                     /plasmid="pCFS3273-3"
                     /geo_loc_name="France"
                     /collection_date="2007-05-03"
     gene            join(5141..6648,1..62)
                     /gene="cea"
                     /locus_tag="C5F73_RS26760"
                     /pseudo=""
     CDS             join(5141..6648,1..62)
                     /gene="cea"
                     /locus_tag="C5F73_RS26760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000447006.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="pore-forming bacteriocin colicin E1"
                     /name="cea"
     gene            448..585
                     /locus_tag="C5F73_RS26770"
                     /old_locus_tag="C5F73_29370"
     CDS             448..585
                     /locus_tag="C5F73_RS26770"
                     /old_locus_tag="C5F73_29370"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405930.1"
                     /GO_component="GO:0019867 - outer membrane [Evidence IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin release lysis protein"
                     /protein_id="WP_001405930.1"
                     /translation="MRKRFFVGIFAINLLVGCQANYIRDVQGGTIAPSSSSKLTGIAVQ
                     "
                     /name="colicin release lysis protein"
     gene            complement(1612..1803)
                     /locus_tag="C5F73_RS26775"
                     /old_locus_tag="C5F73_29375"
     CDS             complement(1612..1803)
                     /locus_tag="C5F73_RS26775"
                     /old_locus_tag="C5F73_29375"
                     /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            1867..2190
                     /locus_tag="C5F73_RS26780"
                     /old_locus_tag="C5F73_29380"
     CDS             1867..2190
                     /locus_tag="C5F73_RS26780"
                     /old_locus_tag="C5F73_29380"
                     /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_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2399..>2830
                     /locus_tag="C5F73_RS27255"
                     /pseudo=""
     CDS             2399..>2830
                     /locus_tag="C5F73_RS27255"
                     /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            2868..3386
                     /locus_tag="C5F73_RS26790"
                     /old_locus_tag="C5F73_29390"
     CDS             2868..3386
                     /locus_tag="C5F73_RS26790"
                     /old_locus_tag="C5F73_29390"
                     /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_000067500.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNNEFRRLGESVSEAVTSNE
                     TKIRDAIALFTASTEESLEKHREGVKEAMMQHRRDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQANLEEIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            3393..3626
                     /locus_tag="C5F73_RS26795"
                     /old_locus_tag="C5F73_29395"
     CDS             3393..3626
                     /locus_tag="C5F73_RS26795"
                     /old_locus_tag="C5F73_29395"
                     /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            complement(3944..4363)
                     /locus_tag="C5F73_RS26800"
                     /old_locus_tag="C5F73_29400"
     CDS             complement(3944..4363)
                     /locus_tag="C5F73_RS26800"
                     /old_locus_tag="C5F73_29400"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016247941.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Exc2 family lipoprotein"
                     /protein_id="WP_001254967.1"
                     /translation="MRRTGNKLCLIAMITATVALTACTPKGSVEQHTRHYVYASDDGFD
                     PNFSTQKADTTRMMVPFFRQFWDMGAKDKATGKSRSDVQQRIQQFHSQEFLNSLRGTTQ
                     FAGTDYRSKDLTPKKSRLLADTISAVYLDGYEGRQ"
                     /name="Exc2 family lipoprotein"
     gene            complement(4444..4881)
                     /locus_tag="C5F73_RS26805"
                     /old_locus_tag="C5F73_29405"
     CDS             complement(4444..4881)
                     /locus_tag="C5F73_RS26805"
                     /old_locus_tag="C5F73_29405"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001405929.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001405929.1"
                     /translation="MGHCHFMAWHTLRDALKMTGRSRSQFYRDMRAGLVSYRTGRDGRR
                     EFETSELIRAYGELKQNETPERHSEGHAENPHDQQTERILRELNELKQCLTLMLEDKQA
                     QDMDRRRQEAEREQLQNEIAQLRQALELEKKRGFWSRLFGR"
                     /name="hypothetical protein"
     Typing          1442..1527
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="8.58e-38"
     Typing          complement(871..1416)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.438"
                     /coverage="98.0"
                     /evalue="0.0"
     Typing          2181..3730
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.473"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttctatgctc ctatattgat aagaataaac ttaatactat aaatgaggtg ttagggattt
       61 aattattctt tattgatata aaaagtccta gcaatccaaa tgggattgct aggaccaaac
      121 aaagtagatt atatagcata aataggttta attttgctac gggggcgtta tttaggtttt
      181 ttcttctttc gaaaaaatct ttctttatga agttaaaagc tatgtattca atagcatatt
      241 ttgaatatgg acatagaata gtgcttatca ctattgcata tagcatctta tctgacacaa
      301 ggaaataata cccttcgctg ttttttgtta taaggtatat atatataagt gtgcagtaca
      361 ggccaaataa aatatttttt atgtagtatc ttaagctcat aaattaaacc tcgccatata
      421 ttcttttcat tttataagga tcgagttatg aggaaaagat tttttgtggg aatattcgcg
      481 ataaacctcc ttgttggatg tcaggctaac tatatacgtg atgttcaggg agggaccatc
      541 gcaccatcct cctcttctaa actgacgggg atcgcggttc agtagaaaag attaaaggat
      601 cttcttgaga tccttttttt ctgcgcgtaa tctgctgctt gcaaacaaaa aaaccaccgc
      661 taccaacggt ggtttgtttg ccggatcaag agctaccaac tctttttccg aaggtaactg
      721 gcttcagcag agcgcagata ccaaatactg tccttctagt gtagccgtag tcgggccact
      781 acttcaagaa ctctgtagca ccgtttgtgc catcatcgct ctgctaatcc ggttaccagt
      841 ggctgctgcc agtggcgtta aggcgtgcct taccgggttg gactcaagac gatagttacc
      901 ggataaggcg cagcggtcgg gctgaacggg gggttcgtgc acacagccca gcttggagcg
      961 aacgacctac accgaactga gataccaaca gcgtgagcta tgagaaagcg ccacgcttcc
     1021 cgaagggaga aaggcggaca ggtatccggt aagcggcagg gtcggaacag gagagcgcac
     1081 gagggagctt ccagggggaa acgcctggta tctttatagt cctgtcgggt ttcgccacct
     1141 ctgacttgag cgtctatttt tgtgatgctc gtcagggggg cggagcctat ggaaaaacgc
     1201 ctgctacgtg gccttcttcc tgttcctggt cttttgctca catgttcttt ccggccttat
     1261 cccctgattc tgtggataac tgtgttaccg tttttgtgtg agtcagtacc gctcgccgca
     1321 gtcgaacgac cgagcgtagc gagtcagtga gcgaggaagc ggaaaagcgc cggaacgtgc
     1381 attttctcct tacgcatctg tgcggcattt cacaccgcat atggtgctct tttcttacaa
     1441 tctgcactga tgccgcatgg ttaagccagt atacactccg ctatcgctac gtgactgggt
     1501 cagggctgcg ccccgacacc cgctaaaacc tgctgacgcg ccctgacggg cttgtcagct
     1561 cccggcatcc gctcacagac aagctgtgac cgtctccggg agctgcatgt gtcagaggtt
     1621 ttcaccgtca tccccgaaac gtgcgaggca gctgcggtaa agctcatcgg cgtggtcgtg
     1681 aagcgattca caaatatcgg cctgttcatc tgcgtccagt tcgttaagct tctccagcag
     1741 cgttaatgtc tggcttctga taaagcgggc catgttaagg gcggtttttt cctgtttagt
     1801 cactgatgcc tccgtgtaag ggggatttct gttcatgggg taatgatacc gatgaaacgc
     1861 gagaggatgc tcacaatacg ggttactgat gatgaacatg cccggttact tgaacgctgt
     1921 gagggtaaac aactggcggt atggatgcgg cgggtctgcc tgggggagcc ggttgcccgt
     1981 tccggaaaac tgccgacact ggcaccgccg ttactgcgtc agctggccgc catcggaaat
     2041 aacctgaatc agacagcccg taaggtgaac agcgggcagt ggtcttccgg tgaccgggtt
     2101 caggtggtgg ccgcactgat ggccatcggg gatgagctgc gccggctgcg tctggctgtc
     2161 agggaacagg gggcgcggga tgatagttaa atttcatgcc aggggaaaag gtggtggcag
     2221 tggtccggtt gattacctgc tggggaggga gcgtaaccgc gaaggcgcaa cggtgcttca
     2281 gggtaatccg gaagaagtcc gggaactcat cgatgccacg ccatttgcga agaaatacac
     2341 gtccggtgtt ctgtcgttcg cggagaagga gctgccgccg ggaggacgtg aaaaagtgat
     2401 ggcgagcttt gagcgtgtac tgatgcccgg tctcgaaaaa aatcagtaca gcatcctgtg
     2461 ggtggagcac caggacaagg gacggcttga gctgaatttt gtcattccga acatggagct
     2521 acagaccgga aaacgcctcc agccgtacta cgaccgcgca gacaggccta gaattgatgc
     2581 ctggcagacg ctggtaaatc accattacgg gctgcatgac ccgaacgccc cggagaaccg
     2641 caggacgctg acactccctg ataacctgcc tgaaacgaaa caggcgcttg ctgagggcgt
     2701 cacgcgaggt atagatgcac tttaccatgc cggagagata aaaggccgtc aggatgtgat
     2761 tcaggcgctc actgaggcgg ggctggaagt ggtcagggtg acgcgaagca gtatcagcat
     2821 tgcagatccg aacggcggga agaatatcag gctgaaagga gcattttatg agcaatcttt
     2881 tgcagacggg cgcggagttc gagaaaaagc tgaaagagag agccgaatct acagagaaaa
     2941 tgctgaacaa cgagttcagg aggctcggcg aatctgtaag cgaggctgtg acatcaaacg
     3001 agacgaaaat cagagacgct atagccctgt tcacagcctc gacagaggaa tcgctggaaa
     3061 aacaccggga aggggtgaaa gaggcgatga tgcagcacag gagggacgtg ttaaagctgg
     3121 cagggaatac gggcatgatg ttactgggga tagtctttct cctgtttacc gcgagtggcg
     3181 ggacgctctg gtatcttgga gggaggatac aggcgaacct ggaagaaatc aggaagcagg
     3241 aagagacatt gcagaaactg aacgcgaaga catggggcgt ggagtttgtg caggacggga
     3301 acaggaaatt ccttgtcctt ccgtacggga aatcagcgga ggtgattccc tttcagggga
     3361 aagagtgggt acatctgaag gagtgacaca gagtgacaga gctggaaaca catttgctga
     3421 acgccttaga gcagctgcaa caggactata tgcagcggct gagcgaatgg gagagcgcct
     3481 tcgtggaatt gcagaagatg ttttcgctta cgcaacggga caacgcgatg ctgaacgagc
     3541 gggtcatgca gttgagtcag caggtgcagc acttgagcga gcagacagaa cgcttgagcc
     3601 agttatacag cgagaactgg agataagaga ggaacggctg atacaggagc gcgaacatgt
     3661 gttatccctg gaacgggagc gtcagccgga aatacaggaa cgcacgctgg atggcccttc
     3721 gctgggatgg tgaaaccatg aaaaatggca gcttcagtgg attaagtggg ggtaatgtgg
     3781 cctgtaccct ctggttgcat aggtattcat acggttaaaa tttatcaggc gcgatcgcgg
     3841 cagtttttcg ggtggtttgt tgccattttt acctgtctgc tgccgtgatc gcgctgaacg
     3901 cgttttagcg gtgcgtacaa ttaagggatt atggtaaatc cacttactgt ctgccctcgt
     3961 agccatcgag ataaaccgca gaaatcgtgt cagccagcag cctggatttt ttcggggtaa
     4021 ggtctttgct gcggtaatca gtacccgcaa attgagttgt gccccggagt gagtttaaaa
     4081 attcctggct gtgaaactgc tgaatgcgtt gttgcacatc actccgtgat tttcctgtcg
     4141 ctttatcttt agctcccata tcccagaact gccgaaaaaa aggcaccatc attcgtgttg
     4201 tgtcggcttt ttgggtggaa aagttgggat caaaaccgtc atcagaagca tatacgtaat
     4261 gccgggtatg ttgttccacg ctgccctttg gggtacaggc tgtgagagct actgttgctg
     4321 ttatcatggc gataagacaa agtttgtttc cggtacgtct catgagtgtc tccctacctt
     4381 aaagtattta ttctcggtga gttattatcc gaagactatt ttatcatcag tctctgacag
     4441 cgttcagcga ccgaacaacc tggaccagaa tccccgtttc ttttccagtt ccagtgcctg
     4501 cctgagctgg gctatctcat tttgtagctg ttcccgttct gcttcctggc gtctgcgatc
     4561 catatcctgt gcctgtttat cctcaagcat cagcgtcagg cattgtttca gctcattcag
     4621 ttcccggaga atgcgttctg tctgctgatc atgtggattt tctgcatgtc cctcactgtg
     4681 cctttctggt gtctcattct gctttaattc gccgtatgcc cggatcagtt cactggtttc
     4741 aaactcccgt cgtccgtccc tgccggtacg gtaactgaca aggcctgcgc gcatatcacg
     4801 gtaaaactgt gaacgcgatc tgcctgtcat ttttagtgcg tcccggagtg tgtgccatgc
     4861 cataaagtga cagtgtccca tagatgtctc atctcatagt ttcagtaaaa cataatgagg
     4921 tctgagaacg gtaatgtttg tgctggtttt tgtggcatcg ggcgagaata gcgcgtggtg
     4981 tgaaagactg tttttttgat cgttttcaca aaaatggaag tccacagtct tgacagggaa
     5041 aatgcagcgg cgtagctttt atgctgtata taaaaccagt ggttatatgt acagtattta
     5101 tttttaactt attgttttaa aagtcaaaga ggattttata atggaaaccg cggtagcgta
     5161 ctataaagat ggtgttcctt atgatgataa gggacaggta attattactc ttttgaatgg
     5221 tactcctgac gggagtggct ctggcggcgg aggtggaaaa ggaggcagta aaagtgaaag
     5281 ttctgcagct attcatgcaa ctgctaaatg gtctactgct caattaaaga aaacacaggc
     5341 agagcaggct gcccgggcaa aagctgcagc ggaagcacag gcgaaagcaa aggcaaacag
     5401 ggatgcgctg actcagcgcc tgaaggatat cgtgaatgag gctcttcgtc acaatgcctc
     5461 acgtacgcct tcagcaacag agcttgctca tgctaataat gcagctatgc aggcggaagc
     5521 agagcgtttg cgccttgcga aagcagaaga aaaagcccgt aaagaagcgg aagcagcaga
     5581 aaaggctttt caggaagcag aacaacgacg taaagagatt gaacgggaga aggctgaaac
     5641 agaacgccag ttgaaactgg ctgaagctga agagaaacga ctggctgcat tgagtgaaga
     5701 agctaaagct gttgagatcg cccaaaaaaa actttctgct gcacaatctg aagtggtgaa
     5761 aatggatgga gagattaaga ctctcaattc tcgtttaagc tccagtatcc atgcccgtga
     5821 tgcagaaatg aaaacgctcg ctggaaaacg aaatgaactg gctcaggcat ccgctaaata
     5881 taaagaactg gatgagctgg tcaaaaaact atcaccaaga gccaatgatc cgcttcagaa
     5941 ccgtcctttt tttgaagcaa ccagacgacg ggttggggcc ggtaagatta gagaagaaaa
     6001 acaaaaacag gtaacagcat cagaaacacg tattaaccgg ataaatgctg atataactca
     6061 gatccagaag gctatttctc aggtcagtaa taatcgtaat gccggtatcg ctcgtgttca
     6121 tgaagctgaa gaaaatttga aaaaagcaca gaataatctc cttaattcac agattaagga
     6181 tgctgttgat gcaacagtta gcttttatca aacgctgact gaaaaatatg gtgaaaaata
     6241 ttcgaaaatg gcacaggaac ttgctgataa gtctaaaggt aagaaaatcg gcaatgtgaa
     6301 tgaagctctc gctgcttttg aaaaatacaa ggatgtttta aataagaaat tcagcaaagc
     6361 cgatcgtgat gctattttta atgcgttggc atcggtgaag tatgatgact gggctaaaca
     6421 tttagatcag tttgccaagt acttgaagat tacggggcat gtttcttttg gatatgatgt
     6481 ggtatctgat atcctaaaaa ttaaggatac aggtgactgg aagccactat ttcttacatt
     6541 agagaagaaa gctgcagatg caggggtgag ttatgttgtt gctttacttt ttagcttgct
     6601 tgctggaact acattaggta tttggggtat tgctattgtt acaggaat
//
