LOCUS       NZ_CP050033             4608 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain 33-6 plasmid pCD33-6-2, complete sequence.
ACCESSION   NZ_CP050033
VERSION     NZ_CP050033.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14278028
            Assembly: GCF_014075915.1
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  JOURNAL   Unpublished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 04:49:25
            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)                     :: 4,601
            CDSs (total)                      :: 4,483
            Genes (coding)                    :: 4,266
            CDSs (with protein)               :: 4,266
            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)              :: 217
            CDSs (without protein)            :: 217
            Pseudo Genes (ambiguous residues) :: 0 of 217
            Pseudo Genes (frameshifted)       :: 50 of 217
            Pseudo Genes (incomplete)         :: 155 of 217
            Pseudo Genes (internal stop)      :: 39 of 217
            Pseudo Genes (multiple problems)  :: 28 of 217
            Pseudo Genes (short protein)      :: 4 of 217
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP050033.1.
            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="33-6"
                     /host="broiler chicken"
                     /db_xref="taxon:562"
                     /plasmid="pCD33-6-2"
                     /geo_loc_name="China:Sichuan"
                     /collection_date="2019-05-11"
     gene            complement(221..1378)
                     /locus_tag="G9P48_RS22700"
                     /old_locus_tag="G9P48_22735"
     CDS             complement(221..1378)
                     /locus_tag="G9P48_RS22700"
                     /old_locus_tag="G9P48_22735"
                     /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            complement(1368..2285)
                     /gene="estT"
                     /locus_tag="G9P48_RS22705"
                     /old_locus_tag="G9P48_22740"
     CDS             complement(1368..2285)
                     /gene="estT"
                     /locus_tag="G9P48_RS22705"
                     /old_locus_tag="G9P48_22740"
                     /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            complement(2997..4490)
                     /locus_tag="G9P48_RS22720"
                     /old_locus_tag="G9P48_22755"
     CDS             complement(2997..4490)
                     /locus_tag="G9P48_RS22720"
                     /old_locus_tag="G9P48_22755"
                     /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_001120888.1"
                     /translation="MPHVAARTASRDRDTGRYQSHRPEQTLLYQIVDEYYPAFAALMAE
                     QGKELPGYVQREFEEFLQCGRLEHGFLRVRCESCHAEHLVAFSCKRRGFCPSCGARRMA
                     ESAALLVDEVLPEQPMRQWVLSFPFQLRFLFASRPEIMGWVLGIVYRVIATHLVKKAGH
                     THQVAKTGAVTLIQRFGSALNLNVHFHMLFLDGVYVEQSHGSARFRWVKAPTSPELTQL
                     THTIAHRVGRYLERQGLLERDVENSYLASDAVDDDPMTPLLGHSITYRIAVGSQAGRKV
                     FTLQTLPTSGDPFGDGIGKVAGSSLHAGVAARADERKKLERLCRYISRPAVSEKRLSLT
                     RGGNVRYQLKTPYRDGTTHVIFEPLDFIARLAALVPKPRVNLTRFHGVFAPNSRHRALV
                     TPAKRGRGNKVRVADEPATPAQRRASMTWAQRLKRVFNIDIETCSGCGGAMKVIACIED
                     PIVIKQILDHLKHKAETSGTRALPESRAPPAELLLGLFD"
                     /name="IS91-like element ISVsa3 family transposase"
     ARG             complement(225..1378)
                     /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 cactcaatag ttggcacaaa gtcctattct aggcactacc attactttac aacgcctgaa
       61 gaaaagagga tatgtttcct taactgaatt acatttacaa cttaacccat ctctttgcga
      121 accgccgagt acgtgacccg tacgctcggt ggtgtgagag gcgcactccg tcagttactg
      181 gcggagccgt ctactcgatt atgtgccgtt ttattccatt ttatacattt aacaattgct
      241 gaaacgtaaa gtcgggttta aacatttcaa tttcgttttg agttgattct tcttgtgctt
      301 ctttgccata gataaacatt tgctgttcat aattttcaat agcctcttca atgctgttaa
      361 atttcccatt ggtcagatta tccgacaata tcaaggcatc catcaacccg ctgtttacgc
      421 cttgtcctgc aaaaggaggc atcaaatgag cagcatctcc aatcatcgtt atgggtaatg
      481 gacgcttact tttccaagac ttacctaagg gaaatattcg tgtcgctaac cctacaaaag
      541 atgatgtcac acgaatcagt tctttgtagc gttcgtccca atcggaaaat tctttcagaa
      601 gaaaatcaac gacactattt ctgttttgaa aatctacctg cgtttggttt ttccattcat
      661 caggtgtttt aaaacttatt ccaaaatgca atgcaccatt attattagga ttcgcaaata
      721 ataaattacc ttgatgagca gccattagcc ggtttccatt gcatagctga aaaaatccag
      781 gacagttcac ctctggatga tgaatatcgg cttgtatatt gaaagtacct gtttcttcaa
      841 cttccgtgtc ggtaacaaat tttcttactt tagacattcc accattggca ataataacca
      901 gatctgctgt ttcactcggt ttattctcaa aagttagtgt ccacttcttc ttaccaggtt
      961 caagcataac aagttttcta tcccaaataa ccgtgtcgtt ttctaaacta ttcaacaaga
     1021 tagcccttaa gtcatttctg tttatttcag gattgtcaaa tcgattttcg ggctttacat
     1081 tttttgtgga taaaatattg cctttttcat cagcaatatt tacacccatt ggtaaggcta
     1141 agtcataata agtttgtaac aatcccgctt ttttcattgc ttcctgacct gaacctttgt
     1201 gtaggtcaag ggttccacca aaaattcttg cctctcggtc gttgtctctt tcgtaaactg
     1261 aaacgtctat gccgttttgc tgtaataatt ttgccatagt cagtccaacg ggtccaccac
     1321 caattattgc aacgttctta tcactaagta aattcatttg tttttcttta ttgctcattt
     1381 atatgttttt caattccgtc aattattgtt gtccaatctt caaagtgcaa ttcgtgtcct
     1441 gttccttcaa gagtaattaa tttcgtattt tgtattttct caattaatac accagcgttt
     1501 ttatagtgcc aaattttgtc atctgttccg tgaattatca aggttggttg atttacttca
     1561 tttagtctat tccaatattc ttcactacct tgcaatgtag cgtgattgaa catacttata
     1621 taattgtttg ctctattgaa ctcagctctt atcagctttt cacttctttg tttatcaaat
     1681 tgtttcttgc cgcacattaa ttctgcaccc tgaattaaat agtttaccac actgtcttca
     1741 tttgaccaat cgactgtgcc tgctttacca tggaaatcta aaatacgtgt gtccatctca
     1801 ggaatagttg ggtccgagtc tccccaaggg cctgtagaca taagtgttaa tgagctaact
     1861 ctatcggcaa actttatagc tgctatttgt gtaattagcc cacctaatga catacccaca
     1921 aaatgtgctt tgtctatttc atagccgtcc aaaattgcaa tggcatcatt tgttaagtca
     1981 acaatgtcgt atggtgctga acccggctca taattagtgg attttcctac atctctgttg
     2041 tcgtaacgaa taacaaaaaa tcctttttca gataattgtt ggcaaaattc agtgtcccaa
     2101 tacagcattg atacggttgc acctgctacc aaaaggattg ctggattttt cttatttcca
     2161 aaactttccg tacagagttc aatgccgttt gttttaatta ttttctcttt catttctgtt
     2221 ttcctttgtt tgcaactgat tattatcagt cctaaaatta atatccaaag tagttttttt
     2281 ttcatttatc aatgtttaac tgttatgctg gtatctttca caatgcccgc taacttatat
     2341 atatacgaaa cattctactc tatttcatac ccatatggca agataggcga atgtttttac
     2401 tattttattt cgcattttga atttctcaaa tataaaaatt attttaacat tttagtactt
     2461 atagtgctta attatttatg tttcaaatct tatgaaatca tataatatat aaaaatatat
     2521 gtatatataa atatattaaa gttgtgtcaa atgttaaaat ttaaaattaa cagaaaaagg
     2581 agtttatagt tagtaaaaaa tttataactt gggttttgaa aaagaaaatc catgaaaaag
     2641 aaattaattt atatgtcgat agcgaccttt gctatcgcac agagttctat tgctcagaac
     2701 cttgatttac agacaccagc aaacaatctt aagcaacaaa tttcatcaat atttcctatt
     2761 gacgtatagg aagaataaac gcccttttca cccaagtcca acagctttgg accgcagttg
     2821 actctttcga cacccctgcg atgcaaccca atccggctga cggggagcca gcaacgctga
     2881 aaatttaccc tcctctttcc cactagcggc tccttttccg acaaccagca cggcggatcc
     2941 ctgccgcggc gctgtgaacg cagcattttg attggtatcg ttggccttca ggctcgtcag
     3001 tcaaacagac ccaggagcag ctcagccggt ggcgcccggc tttcgggtaa cgccctggtc
     3061 ccgctggttt cggctttgtg cttcaggtga tcaaggatct gcttgatcac tatagggtct
     3121 tcaatgcagg cgatgacttt catggcgccg ccgcagccgc tgcaggtctc gatgtcgata
     3181 ttgaaaacac gcttgagccg ttgcgcccat gtcatcgacg ctcgccgttg tgctggtgtt
     3241 gccggttcat cagccaccct gaccttgttg cccctgcccc gttttgccgg cgtgaccaac
     3301 gcccggtgcc gactgttggg tgcgaacacc ccgtggaagc gggttaggtt gactctgggc
     3361 ttcggtacca gggcggccag ccttgcaatg aaatccaatg gttcgaaaat gacgtgcgtg
     3421 gtgccgtccc ggtacggcgt cttgagctgg tagcgcacgt tgccgcctcg tgttaacgac
     3481 agccgcttct cggataccgc cgggcggctg atgtaccggc acagccgttc gagcttcttg
     3541 cgttcatcgg ccctggccgc cacgccggcg tgcaggctgg acccggctac cttgccaatc
     3601 ccgtcaccga acggatcacc actggtcggc agagtttgca aagtgaacac ctttcgcccc
     3661 gcctgtgaac cgacagcgat acggtaagtg atcgagtgcc ccagcagggg tgtcatcggg
     3721 tcgtcatcca ccgcatccga ggccagatag ctgttttcga catcccgttc cagcaggcct
     3781 tgccgttcca gatagcgacc cacccggtgg gcgatggtgt gcgtcagctg ggtgagctct
     3841 gggctggtcg gcgccttgac ccagcggaaa cgcgctgagc cgtgggattg ctcgacatac
     3901 acaccgtcga gaaacagcat gtggaagtga acattcagat tgagcgccga tccaaaacgc
     3961 tggatcaggg tgaccgcgcc cgtcttggcc acttggtggg tatggcccgc tttcttgacc
     4021 aggtgcgtgg caatgacgcg gtaaacgatg cccagcaccc accccatgat ctcgggccgg
     4081 ctggcaaaca ggaaacgcag ctgaaacggg aagctcaaca cccactgacg catgggttgt
     4141 tcaggcagta cttcatcaac cagcaaggcg gcactttcgg ccatccgccg cgccccacag
     4201 ctcgggcaga aaccgcgacg cttacagctg aaagcgacca ggtgctcggc gtggcaagac
     4261 tcgcagcgaa cccgtagaaa gccatgctcc agccgcccgc attggagaaa ttcttcaaat
     4321 tcccgttgca catagcccgg caattccttt ccctgctctg ccataagcgc agcgaatgcc
     4381 gggtaatact cgtcaacgat ctgatagaga agggtttgct cgggtcggtg gctctggtaa
     4441 cgaccagtat cccgatcccg gctggccgtc ctggccgcca catgaggcat gttccgcgtc
     4501 cttgcaatac tgtgtttaca tacagtctat cgcttagcgg aaagttcttt taccctcagc
     4561 cgaaatgcct gccgttgcta gacattgcca gccagtgccc gtcactcc
//
