LOCUS       NZ_CP073965             6200 bp    DNA     circular CON 24-AUG-2023
DEFINITION  Escherichia coli strain MB31 plasmid pYLMB31c, complete sequence.
ACCESSION   NZ_CP073965
VERSION     NZ_CP073965.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN18877309
            Assembly: GCF_024585585.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6200)
  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  JOURNAL   Unpublished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 6200)
  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 06:37:15
            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)                     :: 4,983
            CDSs (total)                      :: 4,858
            Genes (coding)                    :: 4,586
            CDSs (with protein)               :: 4,586
            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)              :: 272
            CDSs (without protein)            :: 272
            Pseudo Genes (ambiguous residues) :: 0 of 272
            Pseudo Genes (frameshifted)       :: 90 of 272
            Pseudo Genes (incomplete)         :: 179 of 272
            Pseudo Genes (internal stop)      :: 68 of 272
            Pseudo Genes (multiple problems)  :: 61 of 272
            Pseudo Genes (short protein)      :: 4 of 272
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP073965.1.
            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..6200
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="MB31"
                     /isolation_source="Cloacal sample"
                     /host="Poultry"
                     /db_xref="taxon:562"
                     /plasmid="pYLMB31c"
                     /geo_loc_name="Cuba: Santa Cruz del Norte"
                     /collection_date="2015"
                     /genotype="ST167"
                     /note="Broiler"
     gene            553..1368
                     /gene="sul2"
                     /locus_tag="KFU79_RS24690"
                     /old_locus_tag="KFU79_24465"
     ARG             554..1365
                     /name="sul2"
                     /gene="sul2"
                     /gene_name="sulfonamide-resistant dihydropteroate synthase
                     Sul2"
                     /tool="amrfinderplus"
                     /drug_class="SULFONAMIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            1429..2232
                     /gene="aph(3'')-Ib"
                     /locus_tag="KFU79_RS24695"
                     /old_locus_tag="KFU79_24470"
     ARG             1430..2229
                     /name="aph(3'')-Ib"
                     /gene="aph(3'')-Ib"
                     /gene_name="aminoglycoside O-phosphotransferase
                     APH(3'')-Ib"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     gene            2232..3068
                     /locus_tag="KFU79_RS24700"
                     /old_locus_tag="KFU79_24475"
     CDS             2232..3068
                     /locus_tag="KFU79_RS24700"
                     /old_locus_tag="KFU79_24475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000480972.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /protein_id="WP_000480968.1"
                     /translation="MFMPPVFPAHWHVSQPVLIADTFSSLVWKVSLPDGTPAIVKGLKP
                     IEDIADELRGADYLVWRNGRGAVRLLGRENNLMLLEYAGERMLSHIVAEHGDYQATEIA
                     AELMAKLYAASEEPLPSALLPIRDRFAALFQRARDDQNAGCQTDYVHAAIIADQMMSNA
                     SELRGLHGDLHHENIMFSSRGWLVIDPVGLVGEVGFGAANMFYDPADRDDLCLDPRRIA
                     QMADAFSRALDVDPRRLLDQAYAYGCLSAAWNADGEEEQRDLAIAAAIKQVRQTSY"
                     /name="aminoglycoside O-phosphotransferase APH(6)-Id"
     gene            complement(<3175..3579)
                     /locus_tag="KFU79_RS24705"
                     /old_locus_tag="KFU79_24480"
                     /pseudo=""
     CDS             complement(<3175..3579)
                     /locus_tag="KFU79_RS24705"
                     /old_locus_tag="KFU79_24480"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120888.1"
                     /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="IS91 family transposase"
                     /name="IS91 family transposase"
     gene            complement(3623..4012)
                     /locus_tag="KFU79_RS24710"
                     /old_locus_tag="KFU79_24485"
     CDS             complement(3623..4012)
                     /locus_tag="KFU79_RS24710"
                     /old_locus_tag="KFU79_24485"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000102614.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000102614.1"
                     /translation="MSTELNSGTVGGFGHMGPNDPYNDGHSGSGSSGGSFNGGGNGGHD
                     NSSGSSYTASFGLITGRHPITVPGTKNINSVDLSAVINNIIHHEGARNNMYLDTANNVR
                     VGVTGTGWQCLATAGISAEGKRTFR"
                     /name="hypothetical protein"
     gene            4230..4670
                     /locus_tag="KFU79_RS24715"
                     /old_locus_tag="KFU79_24490"
     CDS             4230..4670
                     /locus_tag="KFU79_RS24715"
                     /old_locus_tag="KFU79_24490"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011161230.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_005119689.1"
                     /translation="MAWHTVQETLKLTGKSRSQLYRDMAKGLVSYRTGKNDRREFETSE
                     LIRAYGELRTSETPKRHKEGHSKSVVSQAENAQLDVIQQKLDALQQTVTLMLEDKMARE
                     AENRLRNEEREQLQAEISRLADALAQEKKRGFWSRLFRSGSE"
                     /name="hypothetical protein"
     gene            complement(5415..5564)
                     /locus_tag="KFU79_RS24720"
                     /old_locus_tag="KFU79_24495"
     CDS             complement(5415..5564)
                     /locus_tag="KFU79_RS24720"
                     /old_locus_tag="KFU79_24495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017880354.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001138880.1"
                     /translation="MPSEYDEQLDSTDTQLPGEYDLFDLMAQVTEENLHAPVDFGSPVG
                     REAL"
                     /name="hypothetical protein"
     ARG             2233..3065
                     /name="aph(6)-Id"
                     /gene="aph(6)-Id"
                     /gene_name="aminoglycoside O-phosphotransferase APH(6)-Id"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          complement(5600..5773)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.429"
                     /coverage="100.0"
                     /evalue="1.19e-84"
     Typing          5697..6199
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.716"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 ccggaaagac acgacaaaac gccactggca gcagccatta gtaacaggag tgcacgagaa
       61 gatagattaa gaggtcttga agtagaggcc tgactgcggc tacactgaaa gaacagtttt
      121 ggtaatggcg gtctcgtgaa ccctgttacc gggttaagca gttccccaac tgacttaacc
      181 ttcgaacaaa ccgcctcccc aggcggtttt ttcgtttaca gagcaagaga ttacgattca
      241 ttgaaaagga tctcaagaag atcctttgta gattactatc aattaatctt ccgaacatga
      301 caccagtcac tgttgattac ggttaaaccg ctccgtaaca ggtttccctc gtattggtga
      361 cttgcagcac caaagaagca aaaaagataa atatatctac ttattgagag atgatatatt
      421 tatttccaaa atgctacaga tacatcatca tgaaacggat caccgcaaac aggttactcg
      481 cctggggatt ccctttcgac ccgagcatcc gtatgagact catgctcgat tattattatt
      541 atagaagccc ccatgaataa atcgctcatc attttcggca tcgtcaacat aacctcggac
      601 agtttctccg atggaggccg gtatctggcg ccagacgcag ccattgcgca ggcgcgtaag
      661 ctgatggccg agggggcaga tgtgatcgac ctcggtccgg catccagcaa tcccgacgcc
      721 gcgcctgttt cgtccgacac agaaatcgcg cgtatcgcgc cggtgctgga cgcgctcaag
      781 gcagatggca ttcccgtctc gctcgacagt tatcaacccg cgacgcaagc ctatgccttg
      841 tcgcgtggtg tggcctatct caatgatatt cgcggttttc cagacgctgc gttctatccg
      901 caattggcga aatcatctgc caaactcgtc gttatgcatt cggtgcaaga cgggcaggca
      961 gatcggcgcg aggcacccgc tggcgacatc atggatcaca ttgcggcgtt ctttgacgcg
     1021 cgcatcgcgg cgctgacggg tgccggtatc aaacgcaacc gccttgtcct tgatcccggc
     1081 atggggtttt ttctgggggc tgctcccgaa acctcgctct cggtgctggc gcggttcgat
     1141 gaattgcggc tgcgcttcga tttgccggtg cttctgtctg tttcgcgcaa atcctttctg
     1201 cgcgcgctca caggccgtgg tccgggggat gtcggggccg cgacactcgc tgcagagctt
     1261 gccgccgccg caggtggagc tgacttcatc cgcacacacg agccgcgccc cttgcgcgac
     1321 gggctggcgg tattggcggc gctgaaagaa accgcaagaa ttcgttaact gcacattcgg
     1381 gatatttctc tatattcgcg cttcatcaga aaactgaagg aacctccatt gaatcgaact
     1441 aatatttttt ttggtgaatc gcattctgac tggttgcctg tcagaggcgg agaatctggt
     1501 gattttgttt ttcgacgtgg tgacgggcat gccttcgcga aaatcgcacc tgcttcccgc
     1561 cgcggtgagc tcgctggaga gcgtgaccgc ctcatttggc tcaaaggtcg aggtgtggct
     1621 tgccccgagg tcatcaactg gcaggaggaa caggagggtg catgcttggt gataacggca
     1681 attccgggag taccggcggc tgatctgtct ggagcggatt tgctcaaagc gtggccgtca
     1741 atggggcagc aacttggcgc tgttcacagc ctatcggttg atcaatgtcc gtttgagcgc
     1801 aggctgtcgc gaatgttcgg acgcgccgtt gatgtggtgt cccgcaatgc cgtcaatccc
     1861 gacttcttac cggacgagga caagagtacg ccgcagctcg atcttttggc tcgtgtcgaa
     1921 cgagagctac cggtgcggct cgaccaagag cgcaccgata tggttgtttg ccatggtgat
     1981 ccctgcatgc cgaacttcat ggtggaccct aaaactcttc aatgcacggg tctgatcgac
     2041 cttgggcggc tcggaacagc agatcgctat gccgatttgg cactcatgat tgctaacgcc
     2101 gaagagaact gggcagcgcc agatgaagca gagcgcgcct tcgctgtcct attcaatgta
     2161 ttggggatcg aagcccccga ccgcgaacgc cttgccttct atctgcgatt ggaccctctg
     2221 acttggggtt gatgttcatg ccgcctgttt ttcctgctca ttggcacgtt tcgcaacctg
     2281 ttctcattgc ggacaccttt tccagcctcg tttggaaagt ttcattgcca gacgggactc
     2341 ctgcaatcgt caagggattg aaacctatag aagacattgc tgatgaactg cgcggggccg
     2401 actatctggt atggcgcaat gggaggggag cagtccggtt gctcggtcgt gagaacaatc
     2461 tgatgttgct cgaatatgcc ggggagcgaa tgctctctca catcgttgcc gagcacggcg
     2521 actaccaggc gaccgaaatt gcagcggaac taatggcgaa gctgtatgcc gcatctgagg
     2581 aacccctgcc ttctgccctt ctcccgatcc gggatcgctt tgcagctttg tttcagcggg
     2641 cgcgcgatga tcaaaacgca ggttgtcaaa ctgactacgt ccacgcggcg attatagccg
     2701 atcaaatgat gagcaatgcc tcggaactgc gtgggctaca tggcgatctg catcatgaaa
     2761 acatcatgtt ctccagtcgc ggctggctgg tgatagatcc cgtcggtctg gtcggtgaag
     2821 tgggctttgg cgccgccaat atgttctacg atccggctga cagagacgac ctttgtctcg
     2881 atcctagacg cattgcacag atggcggacg cattctctcg tgcgctggac gtcgatccgc
     2941 gtcgcctgct cgaccaggcg tacgcttatg ggtgcctttc cgcagcttgg aacgcggatg
     3001 gagaagagga gcaacgcgat ctagctatcg cggccgcgat caagcaggtg cgacagacgt
     3061 catactagat atcaagcgac ttctcctatc ccctgggaac acatcaatct caccggagaa
     3121 tatcgctggc caaagcctta gcgtaggatt ccgccccttc ccgcaaacga ccccaaacag
     3181 gaaacgcagc tgaaacggga agctcaacac ccactgacgc atgggttgtt caggcagtac
     3241 ttcatcaacc agcaaggcgg cactttcggc catccgccgc gccccacagc tcgggcagaa
     3301 accgcgacgc ttacagctga aagcgaccag gtgctcggcg tggcaagact cgcagcgaac
     3361 ccgtagaaag ccatgctcca gccgcccgca ttggagaaat tcttcaaatt cccgttgcac
     3421 atagcccggc aattcctttc cctgctctgc cataagcgca gcgaatgccg ggtaatactc
     3481 gtcaacgatc tgatagagaa gggtttgctc gggtcggtgg ctctggtaac gaccagtatc
     3541 ccgatcccgg ctggccgtcc tggccgccac atgaggcatg ttccgcgtcc ttgcaatact
     3601 gtgtttacat acagtctatc gcttagcgga aagttctttt accctcagcc gaaatgcctg
     3661 ccgttgctag acattgccag ccagtgcccg tcactcccac tcttacattg ttcgcagtat
     3721 ctaggtacat gttattgcgt gcaccttcat gatgtataat gttattaatg acagcagaaa
     3781 gatcgacaga attaatattc ttcgtacctg ggacagttat cgggtgtcgg ccagtgatga
     3841 gaccaaagga tgcagtataa gatgaaccac tactattatc atggccacca ttaccaccac
     3901 cgttaaaact acctcccgaa cttccagagc cgctatgacc atcattgtag gggtcatttg
     3961 gtcccatgtg accaaaacca ccgacagtac cgctatttaa ctctgtactc ataaaattat
     4021 cctctttgac ttttaaaaac agcaaaaact gtatttataa caatgtgttt atatacagta
     4081 ttcgaaatac tacgcccgtc aaaaccacac cgtcaacagg ttttttgtgt atttttcacg
     4141 cctcacgggc agcctcagac cttttgtgtt aaaacagtaa tatgttctgc tgttacaata
     4201 cggtacacac aggagacact gtcactttta tggcatggca cacagttcaa gagacactga
     4261 aattaacagg aaagtcgcgc tcgcaattat atcgtgacat ggctaaaggc cttgtcagct
     4321 atcgcacagg aaaaaatgat cgccgggagt tcgagaccag tgaactgatt cgggcctatg
     4381 gcgagctgcg cacttctgag acaccaaaaa ggcacaagga gggacactcc aaatctgtcg
     4441 ttagccaggc ggaaaatgct cagctagacg tcattcagca gaaactggac gctctgcagc
     4501 agactgttac cctaatgctt gaagacaaga tggcgcggga agcagaaaac cgcctgcgaa
     4561 atgaggagag ggaacaacta caggccgaaa ttagccgtct ggctgacgcg ctggcacagg
     4621 aaaaaaagcg gggattctgg tcgcggctgt ttcgctccgg ttcagagtaa cagtgcaggt
     4681 gactctgatt taccataaca tctgttatca gcaccgcctg agaggccctc agggcgtttc
     4741 tgacgggaaa ccggtaaaac aggcaacaaa ccacccgaaa acccgccaga aacgcgcagg
     4801 ctctgttttt acggcatgca tgagtatgcg cacaagtgca tagcgcggaa attcacacca
     4861 ttcagccggg gtaagtcctg tttccggcgt tcttcccatc cgaaaacggt gaacggggac
     4921 gcaatttatt gcgtggccgt gaagcgttgc cggcgcagcc ggaaaacccg ctgtcagcac
     4981 gttcaggaag ggggtgatgt acaaatggca cagaggatga aagtgacgta tgagctgaag
     5041 gaatgatgta aaagtgatgt ataagtgatg taaaagtgat gtatgaactg aaggagcgat
     5101 gtaattctgt agtcaggaag aataacccgt tcatgcaggc atgaacgata cagtgaggaa
     5161 cgcttttttt gtcacgatct ccccttaacc tgcgtaaatc acccgccatg gttgattatt
     5221 tttcaacctc aaaatggtca tacacctaac gcagccgcga ttttcatcgc aactgcatga
     5281 attaaaagaa aaaaaaggaa tatttcgttt tcacgagtaa tacccgggta ttaaaaatcc
     5341 actgtaatta catgaaaata aagaaataaa aggtaatacc ggagtattac cacgtacgcg
     5401 ggcaagcgaa aaagctataa cgcttcccgg ccgacaggcg acccaaaatc cacaggggca
     5461 tgcaggttct cttcagtaac ctgcgccatt aaatcaaaaa ggtcatattc gccgggaagc
     5521 tgcgtatcag tcgaatccag ttgttcatca tattcagatg gcatggggtg atatccagta
     5581 gctgagaggt tgttagcggg tttcggggcg cagccctgaa ccagtcatgt agcgctagcg
     5641 gagtgtatac tggcttacta tgttgccacg attgcgaaaa tcagtgaagt gcttcatgtg
     5701 gcaggagaaa aaaggcagca ccggcgcgtc agcagaatat gcgatacagg agatattccg
     5761 cttcctcgct cactgactcg ctacgctcgg tcgttcggct gcggcgagcg gtaccggctt
     5821 acggacgggg acggaaattt cctggaagat accaggaaga cacttagcaa agaagagata
     5881 aggccacggc gaagccgttt ttccataggc tccgcccccc tgacaagcat cgcaaaatct
     5941 gacgctcaaa tcagtggtgg cgaaacccga caggactata aagatcccag gcgtttcccc
     6001 ctggtagctc cctcgtgcgc tctcctgttc ctgcctttcg gtttaccggt gtcattccgc
     6061 tgttatggcc gcggtttctc attccacgcc tgacactcag ttccgtgaag gcagttcgct
     6121 ccaagctgga ctgtatgcac gaaccccccg ttcagtccga ccgctgcgcc ttgtccggta
     6181 actatcaact tgagtccaac
//
