LOCUS       NZ_OQ401025             5429 bp    DNA     circular CON 24-MAY-2024
DEFINITION  Escherichia coli strain C40 plasmid pC40_Col, complete sequence.
ACCESSION   NZ_OQ401025
VERSION     NZ_OQ401025.1
DBLINK      BioProject: PRJNA224116
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5429)
  AUTHORS   Menichincheri,G., Polani,R., Arcari,G., Carattoli,A.,
            Guardabassi,L., Damborg,P., Subramani,P. and Pirolo,M.
  TITLE     Genetic background of neomycin resistance in clinical Escherichia
            coli isolated from Danish pig farms
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5429)
  AUTHORS   Menichincheri,G., Polani,R., Arcari,G., Carattoli,A.,
            Guardabassi,L., Damborg,P., Subramani,P. and Pirolo,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-FEB-2023) Molecular Medicine, Sapienza University of
            Rome, Viale di Porta Tiburtina 28, Rome, Lazio 00182, Italy
COMMENT     ##Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 12/12/2022
            Sequencing Technology :: Illumina; Oxford Nanopore Technologies
            ##Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_029538005.1-RS_2024_05_24
            Annotation Date                   :: 05/24/2024 04:08:50
            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)                     :: 8
            CDSs (total)                      :: 8
            Genes (coding)                    :: 7
            CDSs (with protein)               :: 7
            Genes (RNA)                       :: 0
            tRNAs                             :: 0
            ncRNAs                            :: 0
            Pseudo Genes (total)              :: 1
            CDSs (without protein)            :: 1
            Pseudo Genes (ambiguous residues) :: 0 of 1
            Pseudo Genes (frameshifted)       :: 0 of 1
            Pseudo Genes (incomplete)         :: 1 of 1
            Pseudo Genes (internal stop)      :: 0 of 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            OQ401025.1.
            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..5429
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="C40"
                     /isolation_source="post-weaning diarrhea"
                     /db_xref="taxon:562"
                     /plasmid="pC40_Col"
     gene            71..664
                     /locus_tag="P9C54_RS00005"
                     /old_locus_tag="IGGEJAMO_00001"
     CDS             71..664
                     /locus_tag="P9C54_RS00005"
                     /old_locus_tag="IGGEJAMO_00001"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_015959180.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_280956915.1"
                     /translation="MFLKTYEAIHMHALSILPSVARANLATKFSSHLKVIELFNTMQDS
                     QVVVLSSLIEGHHLTSSGNSVKADFEVTRLPAIIEMLEKKYFFPIRHLNVSVKSVTTGR
                     MTGQTVYFIEPEHIEQLLADPELVFANQERSLFFRSLEKEGKNLGKLIEKKGSVSQAVL
                     SLLHHAYKDKPLSDEMWKEIEDKFTHMLDELSAA"
                     /name="hypothetical protein"
     gene            complement(693..1331)
                     /locus_tag="P9C54_RS00010"
                     /old_locus_tag="IGGEJAMO_00002"
     CDS             complement(693..1331)
                     /locus_tag="P9C54_RS00010"
                     /old_locus_tag="IGGEJAMO_00002"
                     /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_280956916.1"
                     /translation="MAVGMSPTLNKQASKERCAVEFATRKKSKTQRKKSKALSYRGLCF
                     FCTLVTGKCQWTSKMSKQDYIQLRTLTDQFYADNKGLQEALDGSNDGKVRGYGIVVIDL
                     NGLVFGIPLRSHLNHKFGFVSERSEGVKKGLDYTKALLIKKEEYVSRAYKIPTPEFTHI
                     NDNKEKIQEDFNKFVNRYIEANVKKDENILRNYRYSTLKNYHKELGLED"
                     /name="hypothetical protein"
     gene            complement(1621..1704)
                     /locus_tag="P9C54_RS00040"
     CDS             complement(1621..1704)
                     /locus_tag="P9C54_RS00040"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /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_071532987.1"
                     /translation="MHEPPVQSDRCAFSGNYRLESNPERHD"
                     /name="replication initiation protein"
     gene            2342..2662
                     /locus_tag="P9C54_RS00015"
                     /old_locus_tag="IGGEJAMO_00003"
     CDS             2342..2662
                     /locus_tag="P9C54_RS00015"
                     /old_locus_tag="IGGEJAMO_00003"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /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_000957082.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGRLPSI
                     SPALLRQLAGMGNNLNQIARKVNTGGAGHDRVQIVAALMAIDAGLERLRHAVLEKGGND
                     DR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2871..>3305
                     /locus_tag="P9C54_RS00020"
                     /pseudo=""
     CDS             2871..>3305
                     /locus_tag="P9C54_RS00020"
                     /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            3340..3825
                     /locus_tag="P9C54_RS00025"
     CDS             3340..3825
                     /locus_tag="P9C54_RS00025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001749519.1"
                     /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_001749519.1"
                     /translation="MSSLLALAKDLEKQSKAQQQNTCEMLKAAFSEHEKSVKAELSASA
                     KRISDAISAHEQGMTAAMQSNRLSVLRMVGRTWLTITLVSVLLIATSGSILWWQGQQIT
                     GNYQTIRAQERTQAMLSEKNHGVQLSLCGEQKLSCVKVNPKAGAYGEEGNWMVLERK"
                     /name="MbeB family mobilization protein"
     gene            3829..4041
                     /locus_tag="P9C54_RS00030"
     CDS             3829..4041
                     /locus_tag="P9C54_RS00030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137423.1"
                     /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_000137423.1"
                     /translation="MTELEKQLLTALEQLHQDYSQRLDEWESAFAEWQKMSGLMQRENA
                     ALNERVTRLSQQVANLSRQLQRLSQ"
                     /name="MbeD family mobilization/exclusion protein"
     gene            4862..5272
                     /locus_tag="P9C54_RS00035"
                     /old_locus_tag="IGGEJAMO_00005"
     CDS             4862..5272
                     /locus_tag="P9C54_RS00035"
                     /old_locus_tag="IGGEJAMO_00005"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000874179.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000874179.1"
                     /translation="MAFISLSNLAAKTGRIIQSQCVTATQTKKSTGAVELGFRLSKSAM
                     DETGITIGDRVDILYDKEENQWMIKKISEGGFGVSGQKNKHGGYSSCAVRLTLRPGFPR
                     LSEDEEDNKKLLSDDSFTQLSEGVIVFRLDDE"
                     /name="hypothetical protein"
     Typing          2055..2234
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="86.339"
                     /coverage="83.0"
                     /evalue="7.539999999999999e-48"
     Typing          complement(1596..2109)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.217"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          2653..4157
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="93.625"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttgagggatg tgaacacgac attttctatt ctgataggtg cgatgctatt ggctttggtc
       61 tcttaagttt atgtttttaa aaacatatga ggctatacat atgcacgctt tatcaatact
      121 accttcagtt gcccgcgcta acctggcaac taaattctcg tctcatttga aggtgatcga
      181 gctcttcaac acgatgcagg attcccaagt tgttgtcttg tcatcactga tcgaaggcca
      241 tcacctcacc agttctggta acagtgtcaa agccgacttt gaggtcactc gcttaccggc
      301 gattatcgag atgttagaga aaaaatattt tttccctatt cgtcatctaa atgtatctgt
      361 taaatctgta actacaggaa ggatgactgg acaaactgtc tatttcatag agcctgaaca
      421 catcgagcaa cttctcgctg atcctgagct tgtgtttgct aatcaggaaa ggagcctctt
      481 ctttcgttct ctcgaaaaag aagggaaaaa tctcggcaag cttatcgaga aaaaaggtag
      541 tgtttctcaa gccgtcttaa gccttctaca tcacgcctac aaagataaac ctctttctga
      601 cgagatgtgg aaggagatag aagataagtt cacccatatg ctggatgaat tgagcgcggc
      661 gtaaaggcaa gggcggtcgt tagaccgcct ttttagtctt ctaaacctaa ttctttgtga
      721 tagtttttca gcgtagagta acgatagttt ctgagtatgt tttcatcttt cttgacgttc
      781 gcttctatgt atctgtttac gaatttgttg aaatcttctt gtattttttc tttgttatca
      841 ttgatatggg taaattcagg agttggtatc ttataggctc gcgatacata ctcttctttc
      901 ttaattagca acgctttggt gtaatccagt cctttcttaa caccttctga tcgctccgaa
      961 acgaatccaa atttatggtt taaatggctt cgtaagggta tcccgaacac caatccgttg
     1021 agatcaataa ctacgattcc gtagcctctt acttttccat cattactgcc gtcgagagcc
     1081 tcttgtaggc ctttgttatc agcataaaac tggtctgtaa gggttcttaa ctgtatgtaa
     1141 tcctgtttgc tcatttttga tgtccattgg cattttcctg taaccaatgt acaaaaaaag
     1201 caaagccctc tgtaagagag ggctttgctt ttctttcgtt gagtcttgga ttttttacgt
     1261 gtggcgaact ctaccgcaca tctttctttg gaagcttgtt tgtttaacgt ggggctcatt
     1321 cctaccgcca cttctagatt tacttatatc aaaaattata tgtgaagtca atttcgtagc
     1381 tgttcttgac tggacttact ttgccagcgt aatcttctcc tgaaacgaaa aaaccaccct
     1441 ggcaggtggt ttttcgaagg ttatttaatc ctggcagatt atctaaccgt ggtaacagtc
     1501 ttgtgcgaga cgtgtcacca aatccgtcct tccagtgtag cctcagtaag gccaccactt
     1561 caagaactct caatacatct ctcgcacatc atgtttacca gtggccgttg ccaatggcga
     1621 ttagtcgtgt ctttccgggt tggactcaag tcgatagtta ccggaaaagg cgcagcggtc
     1681 ggactgaacg gggggttcgt gcatacagtc cagcttggag cgaactgcct acccggaact
     1741 gagtgtcagg cgtggaatga gataaacgcg gccataacag cggaatgaca ccggtaaacc
     1801 gaaaggcagg aacaggagag cgcacgaggg agccaccagg gggaaacgcc tggtatcttt
     1861 atagtcctgt cgggtttcgc caccactgat ttgagcgtca gatttcgtga tgcttgtcag
     1921 gggggcggag cctatggaaa aacggcagcg ccgcatcctt ttcttgccct gtttgtcatg
     1981 ccgtatgcct ttgctcttat ccgtgtgcag gtaacgcccg ccgcagccga acggcaggag
     2041 cggaagcgac cgagtgagcg aggaggcgta atatcaccgc aacctccatg ttctcccgta
     2101 cgccctgcag ctgcattttc ccctgccaca tgaagcactt ttataaagtg ttactccgcc
     2161 gtaacatatt aagccagtat acactccgct agcgctacgt gactggttca gggctgcgcc
     2221 ccgaaacccg ctaaaagcca ctgacgcgcc tgcggcttgt ccaacaccgt gccgaccggg
     2281 aaacatttcc cgcccgtccc ggtgttatca ggaggctact ctggcagaca aacgcaacaa
     2341 gatgctcacg atgtgggtga cggaagacga acaccggcgg ctgctcgagc ggtgcgacgg
     2401 caagcagctg gcggcgtgga tgcgtcagac ctgcctcgat gagaagccgg cgcgtgccgg
     2461 cagactgccg tcgatatcgc cggcgctgct gcgccagctt gccggtatgg gtaataacct
     2521 gaaccagatc gcccggaaag tgaataccgg tggtgccggt catgaccggg tgcagatcgt
     2581 ggccgccctg atggcaatcg acgcgggact ggagcggctg cggcatgcgg tgctggaaaa
     2641 aggggggaat gatgatcgtt aaattccatc cccgggggcg cggtggtggt gccggtccgg
     2701 tggattacct gctgggaaaa gaccggcagc gcgagggggc gaccgtgctg cagggaaagc
     2761 cggaggaagt ccgggagctt atcgatgcct cgccgtatgc gaaaaagtac acctccggcg
     2821 tactgtcgtt cgcggaggct gagctgccgc ccgggcagcg ggagcagatc atggccagct
     2881 ttgagcgggt tctgatgccc gggctcgata aagaccagta cagcattctg tgggtggagc
     2941 acaccgacaa ggggcggctg gagctgaatt tcctgatccc caacacagag ctgctgaccg
     3001 ggaaacgcct gcagccgtat tacgatcgcg ccgaccggcc gcgcatcgat gcctggcaga
     3061 ccgtggtgaa cggcagactg gggctgcatg atccaaacgc cccgaagaac cggcggttac
     3121 tggtcacgcc gtccgcactg ccggaaacga agctggaagc cgctcaggcg attacacggg
     3181 gtttgctggc cttagcctca tccggggcgc tcaaaacgcg cgaggacgtc acaggggcgc
     3241 tcactgcggc aggttttgag gtggtccgca ccacaaagaa cagtatcagc attgccgacc
     3301 cggacggggg gcgaaacatc cgactgaagg gagccattta tgagcagtct tttagcgctg
     3361 gcgaaggact tggaaaagca atcgaaagcg cagcagcaga atacctgcga gatgctgaaa
     3421 gccgcattca gcgagcacga gaagtctgta aaagcggaac tgagcgcaag cgcgaagaga
     3481 atcagcgacg ccatcagcgc ccacgagcag ggtatgaccg cggcgatgca gtcgaaccgg
     3541 ctgagcgtgc tgcgtatggt tggccggacg tggctgacca tcaccctggt ctcagtactg
     3601 ctgatcgcca cgagcgggag cattctgtgg tggcaggggc agcagatcac cgggaattac
     3661 cagactatcc gggcgcagga gcggacgcag gccatgctgt cggagaagaa ccacggcgtg
     3721 cagctgtcgc tctgtgggga acagaaactg tcctgcgtca aagtgaaccc gaaagcggga
     3781 gcttacgggg aggaagggaa ctggatggta ctggagagga aatagcccat gacggaactg
     3841 gaaaaacagt tgctgaccgc attagagcag ctacatcagg actactcgca aaggctggac
     3901 gagtgggaga gcgccttcgc ggaatggcag aagatgtctg gtcttatgca acgggagaac
     3961 gcggcgctga acgagcgcgt cacgcgcttg agtcagcagg tggcgaactt gagcaggcag
     4021 ttacagcgtt tgagccagta gtgcagcggc atgaaatggc ggtggccgcc gaacgggcat
     4081 acgagcagcg acagcatgaa aaagagctgg cagaaccccg tttccgtcag cggagctata
     4141 acggtccgac gctgggctga ctgcgcgcat ccagtgacaa accccaagaa gaagggctca
     4201 taaatttccc gctaaatacg gtcgtgatga aaagatcacg gctcaagaga gggggattta
     4261 tgaagatact aaaagcgctc agtctgatac tgcaatgcgt caaactggca atggatctgt
     4321 gggagcgatt cgggggaaag tggccttttt agtgctttac accgtattta tacgcgaaaa
     4381 ctgctgtcat tcatctggct gcataaccat gcagccaagt gaaatttatc tggcgtaaac
     4441 ggggcggttt accgggtgct ttgctagggg tttcacccga caggcaccgt atttgcgccg
     4501 aaccagcccg aagcggtgcg ggcaagaact cttatgttaa attcatctca tcggcaacct
     4561 atacaggcat aaaaatcagt ttctataagc ggctttcttg cacctacttg gtgatttttt
     4621 ggatgcgctg acgttgctcg actttaaatc accatagaaa aatacccttt acttacataa
     4681 agatcgatct ggatgtgtat cttgacgagg ttcaatacga gcaattgttt ttatatttaa
     4741 ggtttcttat cgccgttttt tgcggctcta gaaaaatcaa tacaaaagat cttgaaagcc
     4801 acctcgctcc ctgggtacac ttccgtataa gaactgatcg atgtctaaaa cggattgtat
     4861 tatggctttt atctctctat cgaacttggc agcgaagact ggaaggataa tccagtcgca
     4921 gtgtgttacg gccacgcaaa cgaaaaaaag cacgggcgct gtcgagctgg gattccgctt
     4981 gagcaagagc gctatggacg agactggtat taccattggg gatcgtgtcg acattcttta
     5041 cgacaaagaa gaaaaccagt ggatgattaa gaaaattagt gaaggtggct ttggtgtgtc
     5101 tgggcaaaaa aacaagcacg gcggttactc atcgtgtgct gttagattga ccttgcgacc
     5161 aggttttcct cgcctttctg aggatgaaga ggacaacaag aagctacttt ccgatgattc
     5221 attcactcag ctaagtgaag gtgtaatcgt cttcaggctg gatgatgaat aggaaggacc
     5281 aaaaaggaaa ggcagagtta gtgagcgtcg ccaaacaatc gactaactcc gccttcttgt
     5341 caacacatca ctacctttgg aagggtggag tgttatgggc ggcattatgt tcataaactt
     5401 gcattctaat aaagaaaaaa tcgtttctt
//
