LOCUS       NZ_CP050034             3525 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain 33-6 plasmid pCD33-6-3, complete sequence.
ACCESSION   NZ_CP050034
VERSION     NZ_CP050034.1
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 3525)
  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  JOURNAL   Unpublished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 3525)
  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
            CP050034.1.
            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..3525
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="33-6"
                     /host="broiler chicken"
                     /db_xref="taxon:562"
                     /plasmid="pCD33-6-3"
                     /geo_loc_name="China:Sichuan"
                     /collection_date="2019-05-11"
     gene            join(3063..3525,1..232)
                     /locus_tag="G9P48_RS22725"
                     /old_locus_tag="G9P48_22760"
     CDS             join(3063..3309,3309..3525,1..232)
                     /locus_tag="G9P48_RS22725"
                     /old_locus_tag="G9P48_22760"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012477181.1"
                     /ribosomal_slippage=""
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="programmed frameshift; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="IS1 family transposase"
                     /protein_id="WP_094322401.1"
                     /translation="MASVNIHCPRCQSARVYRHGQNPKGRDRFRFRDCHRVFQLTYTYQ
                     ARKPGMKELITEMAFNGAGFRDTARTLKIGISTVIRTFKKLAPTRITSSPVAHADVALI
                     CELDEQWSYVGSKARQHWLWYAYNTKTGGVLAYTFGPRTDQTCRELLALLTPFNIGMLT
                     SDDWGSYGRVVPKNKHLTGKIFPQRIERNNLTLRTRIKRLARKTICFSRSVEIHEKVIG
                     AFIEKHMLY"
                     /name="IS1 family transposase"
     gene            1465..1590
                     /locus_tag="G9P48_RS22730"
                     /old_locus_tag="G9P48_22765"
     CDS             1465..1590
                     /locus_tag="G9P48_RS22730"
                     /old_locus_tag="G9P48_22765"
                     /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_072006160.1"
                     /translation="MHEPPVQSDRCACSGNYRLESNPERHDKAPLAAAIGNLVRR"
                     /name="replication initiation protein"
     gene            2110..2709
                     /locus_tag="G9P48_RS22735"
                     /old_locus_tag="G9P48_22770"
     CDS             2110..2709
                     /locus_tag="G9P48_RS22735"
                     /old_locus_tag="G9P48_22770"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000430080.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="GNVR domain-containing protein"
                     /protein_id="WP_240743510.1"
                     /translation="MSIILFVVFSLILSSIFLLANKNKINIKYELNMIANSPGMIINCG
                     DDFYCKANIIQSIINNKSKSITSNIDERGKKINLSWAGDDRYKPSVTAEVNAIHKAIND
                     WYIQDYKTYKSIINNQDSNYINGTETYAKVSLLTKTNTSGERNFISINNEIVNKKYKPA
                     LIMTLTLIMAIIFSSSYHIIKRSVLEYKNKLNRSFY"
                     /name="GNVR domain-containing protein"
     Typing          1085..1574
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.723"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 ccccttcaac atcggcatgc tcaccagcga tgactggggc agctatggcc gggtggtgcc
       61 gaagaataag catctgaccg gcaaaatatt cccccaacgc attgagcgta ataatctgac
      121 gctacgcacc cgcattaagc ggttggctcg taaaacaatc tgcttctcac gctcagttga
      181 gatccacgaa aaagtgatcg gagcgtttat cgaaaaacac atgctctact aattggatgc
      241 actaccagat tctgaaccgt agatatataa gtctgcattt cagcttcatc aatcccgttt
      301 tttttactga atccatttac caatatcctg tccatacgtt actaaagaaa ataatatata
      361 cggaatgagt tatcatgcgc ctaatttacc ataacatctg ttgcccgcac cctctcagac
      421 agcctcagcg cgtttctggg tcttcctgcc tgtttccggc acttccctgt gcctatatcg
      481 tgaaaaaacg cgcctgatga ttctggcgcg tctgcatggc tatgcacaca catgcatggc
      541 tgggatttta gccgctaaaa tccggcagga cgcccaaaag caccactgaa cctcacgaat
      601 aacgcctcac gggtgcgcag tttactgtgc ggccgtgagg cgttggccag gccgtcaggc
      661 atggctggat ttattgctaa gggggtcgga tttaacgtgg attaatcagc acgcagtgat
      721 gaacgggatt cggaaggggc acccttgcgg cgcggcgatg tatacatcgc taacgtgcct
      781 tggtcattta ttgcaagaag ggagaggtag cattttgata gcaaaaaagt agcaaaaaga
      841 tagcaaacat gcgggagcta accaggagtc tttagcgggc cggcggtact ccaaaaacac
      901 atcttgtccc gctgttttgt gaataagcca gcatagctgt gggcacaaaa catttcctgt
      961 ccgctgcttt aacctttgta atccaggaac gtcaggtgac gtcactttgc ggcgttagcc
     1021 ctatcctgca tcgtattaaa aaatgcagct atggcgcgta cggtgccaaa gataagcccg
     1081 gagatattcc gcttcctcgc tcactgactc gctccgctcg gtcgttcggc tgcggcgagc
     1141 ggtaccggct tactggcggg gcggaaattt ccaggcatct tccaggaaga agcttaacag
     1201 ggaagcaaga aggccacggc gaagccgttt ttccataggc tccgcccccc tgacaagcat
     1261 cacgaaatct gacgctcaaa tcagtggtgg cgaaacccga caggacttaa agataccagg
     1321 cgtttccccc tggtggctcc ctcgtgcgct ctcctgttcc tgcctttcgg tttaccggtg
     1381 tcattccgct gttatggccg cgtttatctc attccacgcc tgacactcag ttccgggtag
     1441 gcagttcgct ccaagctgga ctgtatgcac gaaccccccg ttcagtccga ccgctgcgcc
     1501 tgttccggta actatcgact tgagtccaac ccggaaagac acgacaaagc gccactggca
     1561 gcagccattg gtaacttggt tcgcagatga tttgttagct aaacacgagg ttgctcttga
     1621 agtgtgcgca tcagtacggc tacactggaa ggacagattt ggttgctgtg ctctgcgaaa
     1681 gccagttacc acggttcaga aacttgccgg tttactgaac cttcgaaaaa accaccttgc
     1741 cgggtggttt tttcgttttc agaccaagag attacggctg taacacaaag atctcaagaa
     1801 gatcttaaaa tatgtggaaa ggatacaggc tgataacaac cccctccata gacatgatcg
     1861 aacaaaaaac aaacaaaaaa attgatttta agagtttcct cacccctaaa taataggtaa
     1921 aatgtttttt atttgattgg catttaaaat gaaatatact aaatcagcga aaatattcat
     1981 cacggctatt ttaattttat ttatttattt atcctatact ttaataacta ttgttggtat
     2041 ataaaaatgg aaagcaattc acctgatatt gatttcatcg agttatttct ctttcttaag
     2101 aaaaaaatcg tgagtattat tttgtttgtt gttttctcat taattttgtc atctattttc
     2161 ttgttagcaa acaaaaacaa aataaatata aagtacgaat taaacatgat cgctaattca
     2221 ccaggcatga ttattaactg tggggatgat ttttattgca aagcgaatat tatacaatca
     2281 attataaaca ataaaagcaa gtctataaca tcaaatatag atgaaagagg gaaaaaaata
     2341 aacctgtcat gggctggtga tgaccgttac aaaccctcgg ttaccgctga agtaaacgct
     2401 atccataaag ctattaatga ctggtacatc caagattata aaacttataa aagcataatt
     2461 aacaaccagg atagcaacta tataaatggc actgaaacat atgcaaaagt ttcattatta
     2521 actaaaacaa acacttccgg agaaagaaac tttatttcaa tcaataatga aatagtaaat
     2581 aaaaagtata aaccagcttt gattatgact ctaacgttaa ttatggctat tatcttttcc
     2641 tcctcgtacc atataataaa aagatctgtg cttgaatata aaaataagtt aaataggtct
     2701 ttttattagc ctgtaacgat taataaccgt attctagcaa catccgttac acgcctgatg
     2761 cagaaaagcc cgctaatagc gggcctcccg ataaatctca cgtgaataag ggtagtcaga
     2821 tctatttctt acccttcttg cctaactgat tcctcatggc actgggccaa ctacagcagt
     2881 ttttattccc catgaggaat ccgattggcc acctcgccat ctccattttt aagatacacg
     2941 cataatttca ttagaccatc tacagctaac tgatgccata actcaccttt agcatgaaga
     3001 ttctgggtga tacctctaat tagttgaatc tgatgtataa tactggcttt tgaggttatc
     3061 tcatagccag cgttaatatt cattgtcccc gttgtcagtc agctcgggtt taccgccatg
     3121 gtcagaaccc taaaggccgt gacagatttc gcttccgtga ctgccaccgt gtgtttcagc
     3181 tcacttatac ttatcaagca cgtaagccgg gtatgaaaga gctgatcact gaaatggcct
     3241 ttaatggtgc cgggtttcgc gataccgcca ggacactgaa aattggtatt agcaccgtca
     3301 tccgaacttt aaaaaactcg cgccaacgcg aataacttct tctcctgttg cccatgctga
     3361 tgtggcgctt atctgcgagc ttgatgagca atggagctac gttggcagta aagcccggca
     3421 acactggctc tggtacgcgt acaacaccaa aacaggcggt gtactggcct acacttttgg
     3481 tccccgaacc gatcaaacgt gccgggagct actggcactg cttac
//
