LOCUS       NZ_CP101871             2994 bp    DNA     circular CON 30-SEP-2023
DEFINITION  Escherichia coli strain LP5-1 plasmid pLP5-1-3kb, complete sequence.
ACCESSION   NZ_CP101871
VERSION     NZ_CP101871.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN29932457
            Assembly: GCF_024499245.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2994)
  AUTHORS   Lu,X., Li,R. and Wang,Z.
  TITLE     Widespread prevalence of plasmid-mediated colistin resistance gene
            mcr-1 and transferability in Escherichia coli isolates from Pigeons
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 2994)
  AUTHORS   Lu,X., Li,R. and Wang,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (25-JUL-2022) College of Veterinary Medicine, Yangzhou
            University, Shuangqiao Street, YangZhou, JiangSu 225000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Illumina HiSeq; QitanTech nanopore
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 09/30/2023 03:44:39
            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)                     :: 4,698
            CDSs (total)                      :: 4,582
            Genes (coding)                    :: 4,316
            CDSs (with protein)               :: 4,316
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 266
            CDSs (without protein)            :: 266
            Pseudo Genes (ambiguous residues) :: 0 of 266
            Pseudo Genes (frameshifted)       :: 80 of 266
            Pseudo Genes (incomplete)         :: 170 of 266
            Pseudo Genes (internal stop)      :: 46 of 266
            Pseudo Genes (multiple problems)  :: 29 of 266
            Pseudo Genes (short protein)      :: 4 of 266
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP101871.1.
            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..2994
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="LP5-1"
                     /isolation_source="pigeon"
                     /db_xref="taxon:562"
                     /plasmid="pLP5-1-3kb"
                     /geo_loc_name="China: Jiangsu"
                     /lat_lon="32.25 N 119.01 E"
                     /collection_date="2021-06"
                     /collected_by="Xiaoyu Lu"
     gene            complement(78..269)
                     /locus_tag="NPX81_RS23400"
                     /old_locus_tag="NPX81_23425"
     CDS             complement(78..269)
                     /locus_tag="NPX81_RS23400"
                     /old_locus_tag="NPX81_23425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /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_001041614.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            705..>785
                     /locus_tag="NPX81_RS23405"
                     /old_locus_tag="NPX81_23430"
                     /pseudo=""
     CDS             705..>785
                     /locus_tag="NPX81_RS23405"
                     /old_locus_tag="NPX81_23430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001333247.1"
                     /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="replication initiation protein"
                     /name="replication initiation protein"
     gene            complement(1059..1787)
                     /locus_tag="NPX81_RS23410"
                     /old_locus_tag="NPX81_23435"
     CDS             complement(1059..1787)
                     /locus_tag="NPX81_RS23410"
                     /old_locus_tag="NPX81_23435"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_123906176.1"
                     /translation="MALMVTRRYLLGGEYPSEEFVQASLEKYFFRQGFDIDTGSYIDLI
                     CRDKESRDVVWHIEVKGKTSQPGLDFRTCLGQLVQRMTKDNINYAIAVPRIKQYERLIE
                     ETSILAVSKLNLHWIFVGPDGSVTIKEPDSSTMKNGNANGNGREVSLVNGGFKRFIPGD
                     FMPTCSYGKAPVVFKSSRREMWDWLDDFVISNGVIPSIADIKEEAESRSGKWTLSNVKI
                     EYQFWKIYHLYKGHFFYQSE"
                     /name="hypothetical protein"
     gene            complement(1858..2157)
                     /locus_tag="NPX81_RS23415"
                     /old_locus_tag="NPX81_23440"
     CDS             complement(1858..2157)
                     /locus_tag="NPX81_RS23415"
                     /old_locus_tag="NPX81_23440"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_023281092.1"
                     /translation="MATATNFDAWLDDVDGDYEEVMALYDSVQNVSDMGLYQCVEGGRG
                     DAWVVSSNHHPEALFLASAVARDTFLKLIRERLCGGEDVDSWYGFQRNISNDHS"
                     /name="hypothetical protein"
     Typing          437..832
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.462"
                     /coverage="92.0"
                     /evalue="2.95e-159"
ORIGIN
        1 gtaataatgt taagcgctaa cacaatgaaa attaaggcga tgccggtatt actccggtaa
       61 tacccagaac ggagccatta cgcaccgtcc tgctgctcat tcaggcgcgc tgacaggctt
      121 cggtaaaggc gttccgcatc ctcatggagt ttctcgcaga aatcagcctc atgatccaga
      181 tccagctcat taagcctgtc cagaagaagc agggactgat cctggatgaa tttagccatg
      241 ttaacggcag tcttttgttg tttgttcatg aaagccccgg cgcgaaagtg cttattgtac
      301 gttctgatgg ttttccgctt cctcgctcat tcgctccctc cgttcggtca tgagtctgcg
      361 gcgagcggag ggaggataag cagataacgt aacggtaagc ataacgaaag ctaaggacaa
      421 gggcgaaaag gccacgcccc gccggggcgt ttttccatag gctccgcccc cctgacaagc
      481 atcacagaat ctgacgctca aatcagtggt ggcgaaaccc gacaggacta taaagatacc
      541 aggcgtttcc ccctggtcgc tccctcgtgc gctctcctgt tccgaccctg ccgcttacca
      601 gatacctgtc cgcctttctc ccttcgggaa gcgtggcgct ttctcatagc tcacgctgtt
      661 ggtatctcag ttcggtgtag gtcgttcgct ccaagctggg ctgtgtgcac gaaccccccg
      721 ttcagcccga ccgctgcgcc ttatccggta actatcgtct tgagtccaac ccggtaagac
      781 acgactaatc gccattgaca acggccactg gtagacagga tgtgcgagag atgtatcgag
      841 agttcttgaa gtggtggcct gactgcggct acactgaaag gacagatttg gtgacatgtc
      901 tcgcacaaga ctgttaccac ggttcagaag ttccccaact tactgaacct tcgaaaaacc
      961 acctccccag gtggtttttt cgttttccga gaaagagatt acgctttgag cgaatgaatc
     1021 tcaagaagat catggcattt gatgaacaaa tgagtcagct actcagattg atagaaaaaa
     1081 tgccccttat acaagtgata tattttccaa aactgatact ctattttaac attagaaagc
     1141 gtccatttcc cactccgcga ttcagcctct tctttaatat cagcaatact tgggatcacc
     1201 ccatttgaaa taacaaaatc gtccaaccaa tcccacattt ctcgccgaga tgatttaaat
     1261 acaacaggag ctttcccata tgagcaagtt ggcataaaat cccccggaat aaatctttta
     1321 aaccctccat tcacaagaga aacttctctt ccattaccat tagcattacc atttttcatc
     1381 gtagagctat caggttcctt aattgtcaca ctgccatcag gcccaacaaa tatccagtgt
     1441 aaattcaatt tactaacagc aagaatgctc gtttcttcta ttaatctttc atactgtttt
     1501 attcttggaa cagcaatagc ataattaata ttatcttttg tcattctctg cactaattgt
     1561 ccaagacaag ttcgaaaatc caaccctggc tgtgatgttt tcccttttac ttcaatatgc
     1621 cacacaacat ccctagattc tttatcacga caaataaggt caatataaga tcccgtatct
     1681 atatcgaacc cttgtcgaaa aaaatatttt tctaaagaag cttgaacaaa ttcctcggag
     1741 ggatattcac cacctagtaa gtaccttctc gtcaccataa gagccacaac ccctacgcat
     1801 cctatttact ataacgtcat attttaagag ttcctacaag gggaactctc tgtacgatta
     1861 cgagtgatca ttcgatatat ttcgttgaaa tccataccat gaatcaacat cttcgccgcc
     1921 acatagcctt tctctaatca atttgaggaa agtatcccta gccacagctg atgctagaaa
     1981 aagagcttct ggatgatgat tagagctcac gacccaagca tcaccccgac caccctcaac
     2041 acactgatac aaccccatat cacttacatt ctgaacggaa tcataaagag ccataacctc
     2101 ctcataatcg ccatcaacat catctaacca cgcatcaaaa ttagtagcag tcgccatgcc
     2161 aatcctccat tttttagttt tcaggagtta atttacatag tgataggggc tgttaagcaa
     2221 ataagttttt accttttttg cctcatgctc taaaagtgag caagacaggc atttaccata
     2281 acgtcgcatt acgcgcaccg ctcagacggc ctgagcgcgt ttctgacggg aaaccggtaa
     2341 aacaggcaac aaaccacccg aaaacccgcc agaaacgcgc aggctctgtt tttacggcat
     2401 gcatgagtat gcgcacaagt gcatagcgcg gaaattcacg ccattcagcc ggggtaagtc
     2461 ctgtttccga tgttcttctt acccgaaaac ggtgaacggg gacgcaattt attgcgtggc
     2521 cgtgaggcgt tgccggcaca gccggaaaaa ccattttcag cacgtgcagg aggcccagga
     2581 agagggggcg gatgtacgaa tagctcagag gtcagatctg acgtaaaaat gatgtaaaag
     2641 tgatgtactt ttgatgtaat tctgttgtac acccgcgatc tgacgtaaaa gtgatgtaat
     2701 tttgatgtac ttttgatgta attctgttgt acacccgcgt tctggggtaa aagcagatgc
     2761 aattttgtag tttatgtgta gtcgctgaac ccatagggtc atacgagcat gaccctttcc
     2821 cggaaaagga cgctttttag ccagaatcat acttaacctg cggcgccagc actcgggagt
     2881 ggtcgtttta tatactaaaa aatgacatac acctaacgca gctgcgtttt tcatcgcaac
     2941 ttcatgaaaa gtaaataaaa aataaaaaac acagggattc tgggtattac cggg
//
