LOCUS       NZ_CP050051             4608 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain 90-1 plasmid pCD90-1-4, complete sequence.
ACCESSION   NZ_CP050051
VERSION     NZ_CP050051.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14278032
            Assembly: GCF_014075335.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4608)
  AUTHORS   Lv,H. and Cui,Q.
  TITLE     Identification of novel plasmids containing the tigecycline
            resistance gene tet(X4) in Escherichia coli isolated from retail
            chicken meat
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4608)
  AUTHORS   Lv,H. and Cui,Q.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-MAR-2020) College of Veterinary Medicine, China
            Agricutural University, Yuanmingyuan West Road, Beijing 100000,
            China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.3.4
            Genome Representation             :: Full
            Expected Final Version            :: No
            Genome Coverage                   :: 100x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 05:05:57
            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)                     :: 4,777
            CDSs (total)                      :: 4,659
            Genes (coding)                    :: 4,513
            CDSs (with protein)               :: 4,513
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 146
            CDSs (without protein)            :: 146
            Pseudo Genes (ambiguous residues) :: 0 of 146
            Pseudo Genes (frameshifted)       :: 53 of 146
            Pseudo Genes (incomplete)         :: 83 of 146
            Pseudo Genes (internal stop)      :: 33 of 146
            Pseudo Genes (multiple problems)  :: 23 of 146
            Pseudo Genes (short protein)      :: 3 of 146
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP050051.1.
            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..4608
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="90-1"
                     /host="broiler chicken"
                     /db_xref="taxon:562"
                     /plasmid="pCD90-1-4"
                     /geo_loc_name="China:Sichuan"
                     /collection_date="2019-05-15"
     gene            477..1394
                     /gene="estT"
                     /locus_tag="G9P52_RS23690"
                     /old_locus_tag="G9P52_23710"
     CDS             477..1394
                     /gene="estT"
                     /locus_tag="G9P52_RS23690"
                     /old_locus_tag="G9P52_23710"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014937123.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="macrolide hydrolase EstT"
                     /protein_id="WP_094309312.1"
                     /translation="MKKKLLWILILGLIIISCKQRKTEMKEKIIKTNGIELCTESFGNK
                     KNPAILLVAGATVSMLYWDTEFCQQLSEKGFFVIRYDNRDVGKSTNYEPGSAPYDIVDL
                     TNDAIAILDGYEIDKAHFVGMSLGGLITQIAAIKFADRVSSLTLMSTGPWGDSDPTIPE
                     MDTRILDFHGKAGTVDWSNEDSVVNYLIQGAELMCGKKQFDKQRSEKLIRAEFNRANNY
                     ISMFNHATLQGSEEYWNRLNEVNQPTLIIHGTDDKIWHYKNAGVLIEKIQNTKLITLEG
                     TGHELHFEDWTTIIDGIEKHINEQ"
                     /name="estT"
     gene            1384..2541
                     /locus_tag="G9P52_RS23695"
                     /old_locus_tag="G9P52_23715"
     CDS             1384..2541
                     /locus_tag="G9P52_RS23695"
                     /old_locus_tag="G9P52_23715"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014615010.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="tetracycline-inactivating monooxygenase Tet(X4)"
                     /protein_id="WP_094309310.1"
                     /translation="MSNKEKQMNLLSDKNVAIIGGGPVGLTMAKLLQQNGIDVSVYERD
                     NDREARIFGGTLDLHKGSGQEAMKKAGLLQTYYDLALPMGVNIADEKGNILSTKNVKPE
                     NRFDNPEINRNDLRAILLNSLENDTVIWDRKLVMLEPGKKKWTLTFENKPSETADLVII
                     ANGGMSKVRKFVTDTEVEETGTFNIQADIHHPEVNCPGFFQLCNGNRLMAAHQGNLLFA
                     NPNNNGALHFGISFKTPDEWKNQTQVDFQNRNSVVDFLLKEFSDWDERYKELIRVTSSF
                     VGLATRIFPLGKSWKSKRPLPITMIGDAAHLMPPFAGQGVNSGLMDALILSDNLTNGKF
                     NSIEEAIENYEQQMFIYGKEAQEESTQNEIEMFKPDFTFQQLLNV"
                     /name="tetracycline-inactivating monooxygenase Tet(X4)"
     gene            2880..4373
                     /locus_tag="G9P52_RS23700"
                     /old_locus_tag="G9P52_23720"
     CDS             2880..4373
                     /locus_tag="G9P52_RS23700"
                     /old_locus_tag="G9P52_23720"
                     /function="catalyse the transposition of transposable
                     elements or transposons"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001120888.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS91-like element ISVsa3 family transposase"
                     /protein_id="WP_015344975.1"
                     /translation="MPHVAARTASRDRDTGRYQSHRPEQTLLYQIVDEYYPAFAALMAE
                     QGKELPGYVQREFEEFLQCGRLEHGFLRVRCESCHAEHLVAFSCKRRGFCPSCGARRMA
                     ESAALLVDEVLPEQPMRQWVLSFPFQLRFLFASRPEIMGWVLGIVYRVIATHLVKKAGH
                     THQVAKTGAVTLIQRFGSALNLNVHFHMLFLDGVYVEQSHGSARFRWVKAPTSPELTQL
                     THTIAHRVGRYLERQGLLERDVENSYLASDAVDDDPMTPLLGHSITYRIAVGSQAGRKV
                     FTLQTLPTSGDPFGDGIGKVAGFSLHAGVAARADERKKLERLCRYISRPAVSEKRLSLT
                     RGGNVRYQLKTPYRDGTTHVIFEPLDFIARLAALVPKPRVNLTRFHGVFAPNSRHRALV
                     TPAKRGRGNKVRVADEPATPAQRRASMTWAQRLKRVFNIDIETCSGCGGAMKVIACIED
                     PIVIKQILDHLKHKAETSGTRALPESRAPPAELLLGLFD"
                     /name="IS91-like element ISVsa3 family transposase"
     ARG             1385..2538
                     /name="tet(X4)"
                     /gene="tet(X4)"
                     /gene_name="tetracycline-inactivating monooxygenase
                     Tet(X4)"
                     /tool="amrfinderplus"
                     /drug_class="TETRACYCLINE"
                     /identity="100.0"
                     /coverage="100.0"
ORIGIN
        1 caataggaaa tattgatgaa atttgttgct taagattgtt tgctggtgtc tgtaaatcaa
       61 ggttctgagc aatagaactc tgtgcgatag caaaggtcgc tatcgacata taaattaatt
      121 tctttttcat ggattttctt tttcaaaacc caagttataa attttttact aactataaac
      181 tcctttttct gttaatttta aattttaaca tttgacacaa ctttaatata tttatatata
      241 catatatttt tatatattat atgatttcat aagatttgaa acataaataa ttaagcacta
      301 taagtactaa aatgttaaaa taatttttat atttgagaaa ttcaaaatgc gaaataaaat
      361 agtaaaaaca ttcgcctatc ttgccatatg ggtatgaaat agagtagaat gtttcgtata
      421 tatataagtt agcgggcatt gtgaaagata ccagcataac agttaaacat tgataaatga
      481 aaaaaaaact actttggata ttaattttag gactgataat aatcagttgc aaacaaagga
      541 aaacagaaat gaaagagaaa ataattaaaa caaacggcat tgaactctgt acggaaagtt
      601 ttggaaataa gaaaaatcca gcaatccttt tggtagcagg tgcaaccgta tcaatgctgt
      661 attgggacac tgaattttgc caacaattat ctgaaaaagg attttttgtt attcgttacg
      721 acaacagaga tgtaggaaaa tccactaatt atgagccggg ttcagcacca tacgacattg
      781 ttgacttaac aaatgatgcc attgcaattt tggacggcta tgaaatagac aaagcacatt
      841 ttgtgggtat gtcattaggt gggctaatta cacaaatagc agctataaag tttgccgata
      901 gagttagctc attaacactt atgtctacag gcccttgggg agactcggac ccaactattc
      961 ctgagatgga cacacgtatt ttagatttcc atggtaaagc aggcacagtc gattggtcaa
     1021 atgaagacag tgtggtaaac tatttaattc agggtgcaga attaatgtgc ggcaagaaac
     1081 aatttgataa acaaagaagt gaaaagctga taagagctga gttcaataga gcaaacaatt
     1141 atataagtat gttcaatcac gctacattgc aaggtagtga agaatattgg aatagactaa
     1201 atgaagtaaa tcaaccaacc ttgataattc acggaacaga tgacaaaatt tggcactata
     1261 aaaacgctgg tgtattaatt gagaaaatac aaaatacgaa attaattact cttgaaggaa
     1321 caggacacga attgcacttt gaagattgga caacaataat tgacggaatt gaaaaacata
     1381 taaatgagca ataaagaaaa acaaatgaat ttacttagtg ataagaacgt tgcaataatt
     1441 ggtggtggac ccgttggact gactatggca aaattattac agcaaaacgg catagacgtt
     1501 tcagtttacg aaagagacaa cgaccgagag gcaagaattt ttggtggaac ccttgaccta
     1561 cacaaaggtt caggtcagga agcaatgaaa aaagcgggat tgttacaaac ttattatgac
     1621 ttagccttac caatgggtgt aaatattgct gatgaaaaag gcaatatttt atccacaaaa
     1681 aatgtaaagc ccgaaaatcg atttgacaat cctgaaataa acagaaatga cttaagggct
     1741 atcttgttga atagtttaga aaacgacacg gttatttggg atagaaaact tgttatgctt
     1801 gaacctggta agaagaagtg gacactaact tttgagaata aaccgagtga aacagcagat
     1861 ctggttatta ttgccaatgg tggaatgtct aaagtaagaa aatttgttac cgacacggaa
     1921 gttgaagaaa caggtacttt caatatacaa gccgatattc atcatccaga ggtgaactgt
     1981 cctggatttt ttcagctatg caatggaaac cggctaatgg ctgctcatca aggtaattta
     2041 ttatttgcga atcctaataa taatggtgca ttgcattttg gaataagttt taaaacacct
     2101 gatgaatgga aaaaccaaac gcaggtagat tttcaaaaca gaaatagtgt cgttgatttt
     2161 cttctgaaag aattttccga ttgggacgaa cgctacaaag aactgattcg tgtgacatca
     2221 tcttttgtag ggttagcgac acgaatattt cccttaggta agtcttggaa aagtaagcgt
     2281 ccattaccca taacgatgat tggagatgct gctcatttga tgcctccttt tgcaggacaa
     2341 ggcgtaaaca gcgggttgat ggatgccttg atattgtcgg ataatctgac caatgggaaa
     2401 tttaacagca ttgaagaggc tattgaaaat tatgaacagc aaatgtttat ctatggcaaa
     2461 gaagcacaag aagaatcaac tcaaaacgaa attgaaatgt ttaaacccga ctttacgttt
     2521 cagcaattgt taaatgtata aaatggaata aaacggcaca taatcgagta gacggctccg
     2581 ccagtaactg acggagtgcg cctctcacac caccgagcgt acgggtcacg tactcggcgg
     2641 ttcgcaaaga gatgggttaa gttgtaaatg taattcagtt aaggaaacat atcctctttt
     2701 cttcaggcgt tgtaaagtaa tggtagtgcc tagaatagga ctttgtgcca actattgagt
     2761 gggagtgacg ggcactggct ggcaatgtct agcaacggca ggcatttcgg ctgagggtaa
     2821 aagaactttc cgctaagcga tagactgtat gtaaacacag tattgcaagg acgcggaaca
     2881 tgcctcatgt ggcggccagg acggccagcc gggatcggga tactggtcgt taccagagcc
     2941 accgacccga gcaaaccctt ctctatcaga tcgttgacga gtattacccg gcattcgctg
     3001 cgcttatggc agagcaggga aaggaattgc cgggctatgt gcaacgggaa tttgaagaat
     3061 ttctccaatg cgggcggctg gagcatggct ttctacgggt tcgctgcgag tcttgccacg
     3121 ccgagcacct ggtcgctttc agctgtaagc gtcgcggttt ctgcccgagc tgtggggcgc
     3181 ggcggatggc cgaaagtgcc gccttgctgg ttgatgaagt actgcctgaa caacccatgc
     3241 gtcagtgggt gttgagcttc ccgtttcagc tgcgtttcct gtttgccagc cggcccgaga
     3301 tcatggggtg ggtgctgggc atcgtttacc gcgtcattgc cacgcacctg gtcaagaaag
     3361 cgggccatac ccaccaagtg gccaagacgg gcgcggtcac cctgatccag cgttttggat
     3421 cggcgctcaa tctgaatgtt cacttccaca tgctgtttct cgacggtgtg tatgtcgagc
     3481 aatcccacgg ctcagcgcgt ttccgctggg tcaaggcgcc gaccagccca gagctcaccc
     3541 agctgacgca caccatcgcc caccgggtgg gtcgctatct ggaacggcaa ggcctgctgg
     3601 aacgggatgt cgaaaacagc tatctggcct cggatgcggt ggatgacgac ccgatgacac
     3661 ccctgctggg gcactcgatc acttaccgta tcgctgtcgg ttcacaggcg gggcgaaagg
     3721 tgttcacttt gcaaactctg ccgaccagtg gtgatccgtt cggtgacggg attggcaagg
     3781 tagccgggtt cagcctgcac gccggcgtgg cggccagggc cgatgaacgc aagaagctcg
     3841 aacggctgtg ccggtacatc agccgcccgg cggtatccga gaagcggctg tcgttaacac
     3901 gaggcggcaa cgtgcgctac cagctcaaga cgccgtaccg ggacggcacc acgcacgtca
     3961 ttttcgaacc attggatttc attgcaaggc tggccgccct ggtaccgaag cccagagtca
     4021 acctaacccg cttccacggg gtgttcgcac ccaacagtcg gcaccgggcg ttggtcacgc
     4081 cggcaaaacg gggcaggggc aacaaggtca gggtggctga tgaaccggca acaccagcac
     4141 aacggcgagc gtcgatgaca tgggcgcaac ggctcaagcg tgttttcaat atcgacatcg
     4201 agacctgcag cggctgcggc ggcgccatga aagtcatcgc ctgcattgaa gaccctatag
     4261 tgatcaagca gatccttgat cacctgaagc acaaagccga aaccagcggg accagggcgt
     4321 tacccgaaag ccgggcgcca ccggctgagc tgctcctggg tctgtttgac tgacgagcct
     4381 gaaggccaac gataccaatc aaaatgctgc gttcacagcg ccgcggcagg gatccgccgt
     4441 gctggttgtc ggaaaaggag ccgctagtgg gaaagaggag ggtaaatttt cagcgttgct
     4501 ggctccccgt cagccggatt gggttgcatc gcaggggtgt cgaaagagtc aactgcggtc
     4561 caaagctgtt ggacttgggt gaaaagggcg tttattcttc ctatacgt
//
