LOCUS       NZ_CP050050             5128 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain 90-1 plasmid pCD90-1-3, complete sequence.
ACCESSION   NZ_CP050050
VERSION     NZ_CP050050.1
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 5128)
  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  JOURNAL   Unpublished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 5128)
  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
            CP050050.1.
            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..5128
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="90-1"
                     /host="broiler chicken"
                     /db_xref="taxon:562"
                     /plasmid="pCD90-1-3"
                     /geo_loc_name="China:Sichuan"
                     /collection_date="2019-05-15"
     gene            complement(join(5120..5128,1..186))
                     /locus_tag="G9P52_RS23665"
                     /old_locus_tag="G9P52_23675"
     CDS             complement(join(5120..5128,1..186))
                     /locus_tag="G9P52_RS23665"
                     /old_locus_tag="G9P52_23675"
                     /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_072644309.1"
                     /translation="MNKQQQIALNMARFIKSQSLTLLEKLDALDADEQATMCERLHELA
                     EELQNSIQVRFETESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1413..2105
                     /locus_tag="G9P52_RS23670"
                     /old_locus_tag="G9P52_23680"
     CDS             1413..2105
                     /locus_tag="G9P52_RS23670"
                     /old_locus_tag="G9P52_23680"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000550475.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF3800 domain-containing protein"
                     /protein_id="WP_072644306.1"
                     /translation="MHLLYVDESGTPSDPTLNHFVLSGISVFEKQTHWIEQEMNAIAAR
                     FNADDPYERELHGSPMRGGRDGWKNFSFNDRKQAIKDCLALLTQKHRDIRIFACVVPKG
                     ALDGKDVITESFYQISSRFDMYLSRLHHQGATSRGVAIFDKSSTEKSIQSLARTFKDTG
                     YEYGKLRNFSEVPLFLDSKASRLIQLADLVSYSIFRKFEFNDDEFYKIIENRFDYHNGK
                     VHGLYVAH"
                     /name="DUF3800 domain-containing protein"
     gene            complement(2264..2527)
                     /locus_tag="G9P52_RS23675"
                     /old_locus_tag="G9P52_23685"
     CDS             complement(2264..2527)
                     /locus_tag="G9P52_RS23675"
                     /old_locus_tag="G9P52_23685"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010891192.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein L"
                     /protein_id="WP_072644307.1"
                     /translation="MAVYTSETKKFLDSVSHDKTWWTSRYNPADDVPVSGIYRCTVCGK
                     EITSNKDDPFPPQNHHQHSQSQAIKWQLIVRTDTQGNGCGSK"
                     /name="protein L"
     gene            complement(2692..3108)
                     /locus_tag="G9P52_RS23680"
                     /old_locus_tag="G9P52_23690"
     CDS             complement(2692..3108)
                     /locus_tag="G9P52_RS23680"
                     /old_locus_tag="G9P52_23690"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001283459.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_057103209.1"
                     /translation="MSDQKNNLDLQKQTLESKWGKEALSMGWSAIPTSLFFLQGALNMT
                     PTTFNVLLHLIIHWWKPYDWPHPSQESIAVRMGVSSRTVQRSLQELENYGLLTKIRTSK
                     DNPKYKGRNIYDMSLLVKSLNILTPDLNAKLNEK"
                     /name="helix-turn-helix domain-containing protein"
     gene            3456..4130
                     /locus_tag="G9P52_RS23685"
                     /old_locus_tag="G9P52_23695"
     CDS             3456..4130
                     /locus_tag="G9P52_RS23685"
                     /old_locus_tag="G9P52_23695"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001259273.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="NYN domain-containing protein"
                     /protein_id="WP_072644308.1"
                     /translation="MRTIVYVDGFNFYHGLVKRSGYKWLDLYKLFEEQLLPIRSRESQL
                     IQVKFFTAEIKAKFASRGELAHQAQQAYHRALVQIYGDNLQIIKGYYSERQECAMTFNE
                     GHPPSKTDRTTVWKLEEKQTDVRMALEMYRDAIRGEAEQLVLCTNDSDMIPPIEMIKAD
                     RPELKIGIVVPREQDTSRVISSLASLGDWSLPYVSYEALRLALLPDKVPTRRKPILKPN
                     HW"
                     /name="NYN domain-containing protein"
     Typing          complement(208..292)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.393"
                     /coverage="87.0"
                     /evalue="5.15e-16"
     Typing          4963..5044
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.857"
                     /coverage="98.0"
                     /evalue="1.43e-25"
     Typing          complement(4139..4662)
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.604"
                     /coverage="99.0"
                     /evalue="7.85e-161"
ORIGIN
        1 tgtttcactt tcggtctcaa agcgaacctg gatgctgttc tggagctctt ccgcgagttc
       61 gtgcagtcgt tcgcacatgg tcgcctgttc gtcggcatcc agagcatcca gtttttcaag
      121 tagtgtcagg ctctggcttt tgataaatcg cgccatattc agcgcaattt gttgctgttt
      181 gttcaccttc cgttgttctc cgtcagtacc gggtgtcggg tggaccctga ccaggtggta
      241 attgtaagac gttgcgggcg acggtattac aattgcacat cctgtcctgt ttctttaggg
      301 gtcagtttgg atatagagaa ttattgtacg gtaagcctgt tttttgaaca gacttaccta
      361 tagcaatagg gtgtactccc gcgctatacg gcattttcag aggtttgacc ttaatcggat
      421 aacctaaatg cgatactgca agagcgacaa cttaaaagcg atagccactg acgcaaaatc
      481 aaccccttac gaaccaagat tggttaaata atgcgcttaa cgtacaaaaa tttccgatct
      541 ccaaactgac cccttcttcg cctcttatgt ttctcgaatg aatcgatggg gacaggaaat
      601 gttttgtggc caccgccgct tcgccggcac cacaaaactg tcggacaaga tgtgtttttg
      661 gagtaccgcc ggcaccaaaa acatttcatc aggcgcagcc tgataccctg aatttcgtac
      721 gtacgaaatt ttgcttttgt tcagatcgag ggcaggattc gcaaagtgct ggcgtttgta
      781 ctcacatcct ttagacgttg cgatgcagga tagggcagac gccgcaaaat gacgtcattt
      841 gcggtatctg ccccgaaaac agaatgtttt ctcctgagcc tgcagctggc tctcagaacc
      901 cctaccgcct cgcaaagctc gttgctcaac gcctcacgac cgcacagtaa actgtgcacc
      961 cgttcaccgt tatcgatggg gttcagcgag ccttttgagc agttcgcagg attttagccg
     1021 ctaaaattcc ggccaggcat gttcgtgcat agccatgcag atgcgcagaa atcatcaggc
     1081 gcgttttttc acgatatgga cagggaaagg tgccggaaac gcagaggacg cggcagaaac
     1141 gcgctgaggg cctctcaggg ggtgcgggca acagatgtta tggtaaatca gaatgacggt
     1201 gaagaaacta tctgattgaa tttatgttat ttgattgctc atggctatgg tgtgtgtata
     1261 aattatttgg gtaaatatgc acttgcctgt tatcattgat attgagtcag ttcgctgccc
     1321 atagcggtgt atgcgatgtt tatcgcactg gcttgcctaa ttcataaaaa ggccgcgcat
     1381 ttgcgcggcc tttttcgttt aaggagtctt agatgcatct cttgtacgtt gatgagtctg
     1441 gtacaccatc agaccctact cttaatcatt ttgtcctttc tggtatatca gtatttgaaa
     1501 agcaaactca ctggatagag caagagatga atgcaattgc ggctcgattt aatgctgatg
     1561 acccgtatga aagagaattg catggttcac cgatgagagg tggacgagat ggctggaaaa
     1621 atttttcttt caatgacaga aaacaagcga tcaaagattg cttagcactc cttactcaaa
     1681 agcatcggga tattcgcata tttgcatgtg ttgtacccaa gggagcctta gatgggaagg
     1741 atgtaataac agagtctttt tatcaaatat cgtctcgttt cgacatgtat ttaagtcgct
     1801 tacatcacca aggagcaacg tctcgagggg tggccatttt tgataaatcg tcgacagaaa
     1861 aaagtattca atctcttgcc cgtacgttta aagatactgg atatgagtat ggaaaacttc
     1921 gcaacttctc tgaagtacct ttatttttgg attccaaagc gtcaaggctg attcagcttg
     1981 ctgatcttgt gtcgtactca attttcagga agtttgagtt caatgatgat gagttctaca
     2041 aaatcataga gaatcgcttt gactaccata atggtaaagt tcacgggctt tacgtagccc
     2101 actaatggaa tagttgtgaa tacgcactat ctataagtaa gagttccttg tgaccatcga
     2161 cgcgaagccc gctacgcggg ctttttcatg cgtagcgtac aacggatgtt atgtttaatc
     2221 cgtctgaccg ctaggtacaa aaaagcccct aagggctttt gagttattta gaaccacaac
     2281 catttccttg cgtatctgtt ctgacaatta attgccactt gattgcctga ctttggctgt
     2341 gttgatgatg gttttgcggc ggaaacgggt catctttatt gctagttatc tcttttccgc
     2401 aaacagtaca acgatagatc cctgataccg gtacatcgtc agctgggtta tatcgtgatg
     2461 tccaccaagt tttatcgtga gaaacactgt ctaaaaattt tttagtctca gaggtgtata
     2521 cagccatttg cctttccttt ccaaaatgta tagggcggag ggggatcctt tttataagtt
     2581 tggttttttt tagcgttttt caatcatctg gcgatgattg aaaaacgcta aaatagagat
     2641 gctatggtaa atataagctg taatggtctg atttttaaaa ttattttatg gttacttttc
     2701 gttcagtttg gcattaaggt ctggcgtaag aatgtttagt gacttaacta aaagagacat
     2761 atcgtaaatg tttcgccctt tgtacttagg gttgtccttg cttgtacgaa tttttgtaag
     2821 caatccgtaa ttttcaagtt cttggagtga gcgttgaact gttcttgatg aaactcccat
     2881 tctaaccgcg atgctctctt gagatggatg tggccaatca tagggtttcc accagtggat
     2941 gattagatga agtagcacat tgaatgttgt gggggtcata ttgagtgcgc cctgcaggaa
     3001 gaaaagggat gtaggaatgg ctgaccatcc catgcttaac gcctccttcc cccatttaga
     3061 ttcaagtgtc tgtttttgaa ggtctaaatt atttttttga tctgacatat accaacctgc
     3121 taagctgaag tcttcataga agacttcagc ttagcaggtt ggtaaattaa ttcatataat
     3181 tagtacgaca ccatcgcgct tataatatca ttatatttaa ctatacttaa tctacactca
     3241 cctcttggta gcgcgattaa gttacgcagc tcccttgagg ctctaaacct ccctttaggt
     3301 gggcagcgat taagttacgc gtcttccttc aggagcttga aaccgccctc tcggttagtt
     3361 ttaaccctga ggaactacaa cttaaactgt ttgctaacgt tagtttttgt tgttaaaacc
     3421 gcctttagag gcggtttttt tatgcgcgaa ataaaatgag aacaatagtt tacgtagatg
     3481 ggtttaattt ttatcacgga ttggttaagc gttcgggata taagtggtta gatctctata
     3541 aactctttga agaacaacta cttccgataa gatcaagaga gtcacagttg attcaggtga
     3601 agttctttac tgctgagatc aaagcaaagt ttgcttctcg gggtgaattg gcgcaccagg
     3661 ctcagcaagc ctaccatcga gcattagtac agatctatgg cgataaccta cagataatca
     3721 aaggttatta ctcagagcgt caggaatgtg caatgacctt taatgagggg catccgccat
     3781 caaaaacgga tagaacaacg gtctggaagt tagaagaaaa gcagaccgac gttagaatgg
     3841 ctttagaaat gtatcgcgat gcgatccgtg gtgaggcaga acaattggtt ctctgtacta
     3901 acgactcaga tatgataccg ccaatagaaa tgataaaagc cgatcgacct gagttaaaaa
     3961 taggaattgt agtgccaagg gaacaagata ctagtcgagt gattagtagt ctggctagtt
     4021 taggggattg gagcttgcca tatgtatcct atgaagcctt aagattagct ttattgccag
     4081 ataaagtccc cactaggcga aagccaatac tgaagccaaa tcactggtaa acagccggat
     4141 cttcttgtga tccttttact ctcgtcgtaa tctcatgtcc tgcaaacaaa aaaaccaccg
     4201 ctaccaacgg tggtttgttt gccggaatca agagctacca actctttttt ccgaaggtaa
     4261 ctggctttca cggagcgcag ataccaaaac tgtccttcca gtgtagccgc agtcaggcca
     4321 tcacttcaag aactctgtag aagcacttct actactctgc tccgtgaatc ctgttaccaa
     4381 tggctgctgc cagtggcgat aagtcgtgtc tttccggatt ggactcaaga cgatagttac
     4441 cggaaaaggc gcagcagtcg gactgaacgg ggggttcgtg catacagtcc agcttggagc
     4501 gaactgccta cccggaactg agtgtcaggc gtggaatgag acaaacgcgg ccataacagc
     4561 ggagtgacac cggtaaaccg aatggcagga acaggagagc gcacgaggga gccaccaggg
     4621 ggaaacgcct ggtatcttta agtcctgtcg ggtttcgcca cctctgactt gagcgtcgat
     4681 ttttgtgatg ctcgtcaggg gggcgaagcc tatggaaaaa cgccaccggc gctgcctttt
     4741 tccgggtttc gtcttgttgc tcacatgttc tttccggcgt tatcctcgga ttctgtggat
     4801 aactgtatta ccatctttga gtgagcagac accgctcgcc gcagccgaac gaccgagcgt
     4861 agcgagtcag tgagcgagga agcggaagag cgcctgaaca ggcatattct ccttacgcat
     4921 ctgtgcggca tttcactccg gatatggcaa acttttcata caatccgcac tgatgctgca
     4981 tgattaagcc cgtatacact ccgctatctc tacgtgactg gttcagggct tcgccccgaa
     5041 ccccactgac gcgccctgac gggcttgtct gctgccgaaa acgctcgcgg acaagccgtg
     5101 agcgcctccg tcagcttcgt tatgtccc
//
