LOCUS       NZ_CP073938             3175 bp    DNA     circular CON 24-AUG-2023
DEFINITION  Escherichia coli strain MB56 plasmid pYLMB56b, complete sequence.
ACCESSION   NZ_CP073938
VERSION     NZ_CP073938.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18877316
            Assembly: GCF_024585445.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3175)
  AUTHORS   Lopez-Dorta,Y., Brilhante,M., Hernandez-Fillor,R.E., Baez,M.,
            Espinosa,I. and Perreten,V.
  TITLE     Molecular epidemiology of Extended-Spectrum Beta-Lactamase-producing
            Escherichia coli from food-producing animals in Cuba using
            whole-genome sequencing
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3175)
  AUTHORS   Lopez-Dorta,Y., Brilhante,M. and Perreten,V.
  TITLE     Direct Submission
  JOURNAL   Submitted (27-APR-2021) Institute of Veterinary Bacteriology,
            University of Bern, Langgassstrasse 122, Bern 3012, Switzerland
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology :: Oxford Nanopore MinION; Illumina NovaSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 08/24/2023 06:23:20
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,657
            CDSs (total)                      :: 4,532
            Genes (coding)                    :: 4,324
            CDSs (with protein)               :: 4,324
            Genes (RNA)                       :: 125
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 208
            CDSs (without protein)            :: 208
            Pseudo Genes (ambiguous residues) :: 0 of 208
            Pseudo Genes (frameshifted)       :: 62 of 208
            Pseudo Genes (incomplete)         :: 136 of 208
            Pseudo Genes (internal stop)      :: 40 of 208
            Pseudo Genes (multiple problems)  :: 33 of 208
            Pseudo Genes (short protein)      :: 4 of 208
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP073938.1.
            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..3175
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="MB56"
                     /isolation_source="Cloacal sample"
                     /host="Poultry"
                     /db_xref="taxon:562"
                     /plasmid="pYLMB56b"
                     /geo_loc_name="Cuba: Nueva Paz"
                     /collection_date="2014"
                     /genotype="ST5334"
                     /note="Laying hens"
     gene            172..366
                     /locus_tag="KFU61_RS23150"
                     /old_locus_tag="KFU61_22965"
     CDS             172..366
                     /locus_tag="KFU61_RS23150"
                     /old_locus_tag="KFU61_22965"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041630.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAENETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1012..1146
                     /locus_tag="KFU61_RS23295"
     CDS             1012..1146
                     /locus_tag="KFU61_RS23295"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005019281.1"
                     /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_071606675.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPVRHDLTPLAAATGKQDVREMY"
                     /name="replication initiation protein"
     gene            complement(1391..2500)
                     /gene="wzz(fepE)"
                     /locus_tag="KFU61_RS23155"
                     /old_locus_tag="KFU61_22970"
     CDS             complement(1391..2500)
                     /gene="wzz(fepE)"
                     /locus_tag="KFU61_RS23155"
                     /old_locus_tag="KFU61_22970"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001421676.1"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_process="GO:0009103 - lipopolysaccharide biosynthetic
                     process [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LPS O-antigen length regulator Wzz(fepE)"
                     /protein_id="WP_053266246.1"
                     /translation="MKISKVSDEHFSNYNMLPNGNEGIDLFGLISVLWAAKIKIVGVIL
                     FFACIGFLVSFVLPQKWTSSAVVTPAESVQWSELNKELSKLHVLGVDFDINRDNAFDLF
                     IKKFQSVNSLNEYMRSSPYVMEMIKKNNISALELHRAIVELSKNMKSVDDNTSKKNDKS
                     SLYVSWTLSFTAPTSKEAHDVLSGYINYVSSLVVRDLMEDIRNKLEVKTNVEKEILALD
                     EIKIRNQLNADIRRLNYSLEVANAAGIKKPVYSNGQIMKDDPDFPVALGSDGIATKLNI
                     KKSIKDVSELSGELRNRQYVVNQLVVAKVGDVDFMPFQYQLSPTLPVRKDGPSNAIIVI
                     LSSVIGGMLACGYILLRHAMEARKMSVIE"
                     /name="wzz(fepE)"
     Typing          complement(38..136)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          complement(447..533)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="95.455"
                     /coverage="100.0"
                     /evalue="1.14e-31"
     Typing          complement(2833..3081)
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.4"
                     /coverage="86.0"
                     /evalue="9.46e-113"
     Typing          558..1084
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="87.956"
                     /coverage="98.0"
                     /evalue="2.2599999999999997e-176"
ORIGIN
        1 acagcggctg cactgcacag ggattattta tcagttgata tgctgtgcca tgatacgtcc
       61 taaagaaaca ggacaggatg tgcaattgta ataccgtcgc ccgcaacgtc ttacaattac
      121 cacctgctca gggtcccccc gacacccgga actgacggag aacaacggaa ggtgaacaaa
      181 caacaacaaa ctgcgctgaa tatggcgcga tttatcaaaa gccagagcct gacactgctt
      241 gaaaaactgg atgctctgga tgccgacgaa caggcggcca tgtgcgaacg actgcacgaa
      301 ctcgcagaag aactccagaa cagcatccag attcgctttg aggccgaaaa tgaaacagga
      361 acataacgaa gctgacggag gcggtcacgg ctttcccgtg ggcgttttcg tcagcagaca
      421 agcccgtcag ggcgcgtcag ggggttttag cgggtgtcgg ggcgcagcca tgacccagtc
      481 acgtagcgat agcggagtgt atactagctt aattatgcgg cgccagagca gatggtgaga
      541 gaacagcgac atatgaggtg tgaaatgctg cacagatacg taaggagaaa atgcagcttc
      601 cggcgctttt ccgcttcctc gctcactgac tcgctgcgct cggtcgttcg gctgcggcga
      661 gcggtgtctg ctcacgcaaa gacggatata cggttatcca cagaatcagg ggagaacacc
      721 ggaaaaaaca tgtgagcaaa aaagaggccc cgaaaaaagg ccgcgccggt ggcgtttttc
      781 cataggctcc gcccccctga caagcatcac aaaaatcgac gctcaagtca gaggtggcga
      841 aacccgacag gacttaaaga taccaggcgt ttccccctgg tggctccctc gtgcgctctc
      901 ctgttcctgc ctttcggttt accggtgtca ttccgctgtt atggccgcgt tcgtctcatt
      961 ccacgcctga cactcagttc cgggtaggca gttcgctcca agctgggctg tgtgcacgaa
     1021 ccccccgttc agcccgaccg ctgcgcctta tccggtaact atcgtcttga gtccaacccg
     1081 gtaagacacg acttaacgcc attggcagcg gccactggta aacaggatgt gcgagagatg
     1141 tattgagagt tcttgaagtg gcagccttac tgaggctaca ctagaaggac agatttggtg
     1201 acatgtctcg cacaagactg ttaccacggt tcagaagttc cccaacttac tgaaccttcg
     1261 aaaaaccacc tccccaggtg gttttttcgt tttctagagt agaagactac ggctgtaagg
     1321 gaatgatctc aagaagatcc tttgaacttt ttataaaagt tgcttataaa atgatgcatc
     1381 agcacaactt ttactcaatc acactcatct ttctggcctc catggcatga cgtaaaagta
     1441 tatagccaca tgcaagcatc cctccaatga cagaagaaag aattacaatt atggcattac
     1501 ttggcccatc ctttctgacc ggtaacgttg ggctcaattg atactgaaac ggcataaaat
     1561 caacatcccc cactttcgcc acaaccaatt gattcacaac atattgacga tttcgcaact
     1621 ccccactcaa ttccgaaaca tccttgattg attttttgat gttcaattta gttgctatac
     1681 catcagaacc gagagccaca ggaaaatctg ggtcatcctt cataatctga ccattgctgt
     1741 atacaggttt ttttattcca gccgcattag caacctccag tgaataattg aggcgtcgaa
     1801 tatctgcatt cagctggttt ctaattttta tctcatccag tgcaagaatt tctttttcaa
     1861 cattagtttt aacttctagt ttatttctta tatcttccat caaatccctt acaacaaggg
     1921 aagaaacata attaatatac ccagacaaca catcgtgagc ttctttactt gttggagcag
     1981 taaaactcag agtccatgat acatacaatg atgacttgtc gtttttctta ctggtattat
     2041 catcaaccga cttcatattt ttactcaact caacaattgc acgatgcagt tcgagagcgc
     2101 taatgttatt ctttttaatc atctccataa cataaggaga tgatctcata tactcattca
     2161 acgaattaac ggactgaaat ttcttaataa acagatcaaa tgcgttatca cgattgatat
     2221 caaaatccac tcccagaaca tgaagcttag aaagctcctt atttaattca ctccattgaa
     2281 cagactcagc aggagtaacc acagcagaac tagtccattt ttgtggcaaa acaaaagaaa
     2341 caagaaagcc aatacaagca aaaaatagaa tcaccccaac aatttttatt tttgctgccc
     2401 ataaaacgct aatcaagcca aaaagatcaa ttccttcatt accattcggc aacatgttgt
     2461 aattagaaaa atgttcgtca gatacctttg agattttcat tgaaaaaaaa cacaatatat
     2521 taacatatgg tttttttatt ctatcatatg ttaggaaaaa acctaaaaac cattcagcag
     2581 acatttaaca taacatttta ttacgcgcac cgctaaaacg cgctgaacgc gattcagccg
     2641 caaacaccgc aaaaagatat gttttccccg gggtaaaccg gaaaaatgcg tcaggatcgc
     2701 tttcagctca ctgcatagct atgcatgaaa gtgaatgacg atcggtttgg gcgcatacag
     2761 tgcccatgag acacattttc ggacattttc agttcgtgaa tccctgactc attgctacat
     2821 atctgaacag acacccctag cagcgccccc aggggcgtcc tgtaaaaaaa cacaccgcgc
     2881 cgctagcagc actcctaata taagatgatg ttttttatga aaatagtcag taccacccct
     2941 aaaaagcggt gttggcgcag ctacaacacc gcgccgacac cgctttttta aatatcacaa
     3001 agagagcaag aagaactaat ttgtcataac tctctattta taaagaaaaa tcagcaaaaa
     3061 attgtttttg cgtggggtgt gcgcatttca ggcatgagaa cagactcgcg tttttccgga
     3121 gtatcagcgg aattattgat taagaaacac tcgacgcaga gcgaaatttt atgca
//
