LOCUS       NZ_CP080160             4234 bp    DNA     circular CON 17-FEB-2024
DEFINITION  Escherichia coli strain PK8261 plasmid pPK8261-4kb, complete
            sequence.
ACCESSION   NZ_CP080160
VERSION     NZ_CP080160.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN20353475
            Assembly: GCF_019428745.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4234)
  AUTHORS   Li,R., Lu,X., Munir,A., Abdullah,S., Liu,Y., Xiao,X., Wang,Z. and
            Mohsin,M.
  TITLE     Widespread prevalence and molecular epidemiology of tet(X4) and
            mcr-1 harboring Escherichia coli isolated from chickens in Pakistan
  JOURNAL   Sci Total Environ 806 (Pt 2), 150689 (2022)
   PUBMED   34599956
REFERENCE   2  (bases 1 to 4234)
  AUTHORS   Mohsin,M., Li,R. and Lu,X.
  TITLE     Direct Submission
  JOURNAL   Submitted (22-JUL-2021) Colloege of Veterinary Medicine, Yangzhou
            University, Shuangqiao Street, YangZhou, JiangSu 225000, China
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: JAN-2021
            Assembly Method                   :: Unicycler v. 0.4.4
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100.0x
            Sequencing Technology :: Illumina HiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 02/17/2024 08:12:46
            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)                     :: 5,557
            CDSs (total)                      :: 5,437
            Genes (coding)                    :: 5,135
            CDSs (with protein)               :: 5,135
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 302
            CDSs (without protein)            :: 302
            Pseudo Genes (ambiguous residues) :: 0 of 302
            Pseudo Genes (frameshifted)       :: 124 of 302
            Pseudo Genes (incomplete)         :: 205 of 302
            Pseudo Genes (internal stop)      :: 62 of 302
            Pseudo Genes (multiple problems)  :: 78 of 302
            Pseudo Genes (short protein)      :: 5 of 302
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP080160.1.
            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..4234
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PK8261"
                     /isolation_source="chicken"
                     /db_xref="taxon:562"
                     /plasmid="pPK8261-4kb"
                     /geo_loc_name="Pakistan: Faisalabad"
                     /lat_lon="31.50 N 73.02 E"
                     /collection_date="2020-05-11"
                     /collected_by="Mashkoor Mohsin"
     gene            complement(join(3340..4234,1..14))
                     /locus_tag="KZY07_RS27495"
                     /old_locus_tag="KZY07_27500"
     CDS             complement(join(3340..4234,1..14))
                     /locus_tag="KZY07_RS27495"
                     /old_locus_tag="KZY07_27500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_009440807.1"
                     /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_058657849.1"
                     /translation="MSAALQYFEENLPHRPYHTDDPAFGLRISGKGRALLARYIQQNQP
                     HAQHWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNLAVRTAPDASVKV
                     LKYAAAIERALCEKLDADVNYSGLICKNPFHLEWQVMEWREEAYTLDELADYLDLSASE
                     RRSVDKHYGLGRNCHLFEITRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRKFSPEGFSAVQAARGRKGGLAKGEAYEDKRFMALCMLENGYSQ
                     KAIAAMLDVHRNTIRNWAMHK"
                     /name="replication initiation protein"
     gene            complement(461..2680)
                     /gene="mobQ"
                     /locus_tag="KZY07_RS27500"
                     /old_locus_tag="KZY07_27505"
     CDS             complement(461..2680)
                     /gene="mobQ"
                     /locus_tag="KZY07_RS27500"
                     /old_locus_tag="KZY07_27505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001029330.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_154074701.1"
                     /translation="MAIYHLSMKIISRKNGYSAVASAAYRSGSVIPDDRTGLTHDYTRK
                     RGVDDAVILTPVNAPSWCGDRSVLWNAVEKAEQRRNSQLAREIELAIPREISREAAREA
                     VLAFVRENFVSRGMIADVAFHHMDRTNPHAHIMLTTRAVGETGFAGKVRDWNDRALAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKAPGLHLGKAACAMEKRGMETERGEQ
                     NRLINSLNLEIQVSRTRLAVIQVQENVRKRELSDAARRAAEALNLTIPAANASADTLRE
                     FIATLPQECGNAWEMTPEFVAMNGKANDIKREGNALVKERDILEKEMTGLRKARPVASI
                     LSELPLMTWAEPEYRKRQLRFWKLEKQIESLRRTYRAVKERDIPARRQAFETQWNTWIS
                     PGMAELKEKLSAREAERRREEAEAEARRKEQEYDARLKHHDNHRLSRETALAGVITGLG
                     RAREPGTGMITRYMILSNRAGEFTVWGDELADYPQSVHDQVNVYLSPGGAVMVTDIHSG
                     LSESHETLARPERVRMYSGATVRHVLEQMRQGWPSYGFPALPHHWPDNFYFSDDRRPAA
                     SPLPSAHRVDVTAYAAPEQLMPVVFSTERNSRTLNLLLCKGPEEMLVGFVRLEDELRPV
                     LALPSPDYSHLMVSIITENGIHLAGYGEAINRDADTPYPPEPKLMQFRLKGCQDTLFAA
                     INKPEEMPDYLFRQLGFNQTWHEWKRDEQHRQQQRRPGHYRGMSM"
                     /name="mobQ"
     gene            2859..3134
                     /locus_tag="KZY07_RS27505"
                     /old_locus_tag="KZY07_27510"
     CDS             2859..3134
                     /locus_tag="KZY07_RS27505"
                     /old_locus_tag="KZY07_27510"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091757.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_052995416.1"
                     /translation="MSRTLEQKIAEAEARLQRLKAKSRSLDTAQKVIVGAAMLARVRRP
                     EEAQLRAFLLQFLRKEVTRQADVNRLQPLINELEKLPRPPAKPQNG"
                     /name="hypothetical protein"
     Typing          2323..2681
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.444"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          2682..2852
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.674"
                     /coverage="98.0"
                     /evalue="5.58e-78"
     Typing          complement(3521..4234)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.266"
                     /coverage="93.0"
                     /evalue="0.0"
     Typing          complement(465..2680)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.61"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agcgcggcgc tcatgtgtta cgattccttc caggttatcg accgacatcg cccctgtatc
       61 ttcgtgaaag tcttggcgga tctacacgaa tttcaggggc gtttgttttt cagtcgctta
      121 cactacaccc aacggcaaat cctgtcgatc cttcccgaaa aaccgatcca tttaccataa
      181 ctcctgttgt acgtacccct taaaacgctc tcagacgcgt tctgacgcaa aaaacgcaaa
      241 aagacaagga aacaccaggg taaaccagaa aaacgcgtca gaatcgtttt caggagcctg
      301 cataactatg cacgaaagca atgcgcgatc ggtttcgacc gttcagaagc gcgaacgggt
      361 caaaacggca aactttctca tccagaaaac gcctcacggg acgcggaatt ttttcgtgtc
      421 ccgtgagacg ttggcggggt tcggggtgca gccccggata tcacatactc atgccccggt
      481 aatgtccggg gcgtcgttgt tgttgcctgt gctgttcgtc ccgcttccat tcatgccagg
      541 tctgattaaa tccgagttga cggaagagat aatccggcat ctcttccggt ttgttgatgg
      601 cagcaaaaag cgtgtcctga cagcccttaa gcctgaactg catcagcttc ggttccggtg
      661 ggtacggagt atcagcatca cggtttatgg cctcaccgta gcctgccagg tgtatcccgt
      721 tctctgtgat gatgcttacc atcagatgac tgtaatccgg cgacggaagc gcaagaacgg
      781 gacgcagctc gtcctccagg cgcacaaaac cgacaagcat ttcctccggc cctttgcaca
      841 acagcagatt cagcgtcctg ctgtttcgct ctgtcgaaaa gacaacgggc atgagttgct
      901 ccggtgccgc ataagcggtg acgtccaccc ggtgcgctga cggcagcgga gaggctgcgg
      961 gcctgcggtc atcgctgaaa taaaaattat ccggccagtg atgcggcagc gccggaaaac
     1021 cgtaagaggg ccacccctgg cgcatctgtt ccagtacatg ccggaccgtc gcaccggaat
     1081 acattctcac acgctcaggc cgggccagcg tctcatgaga ttctgacagc cccgaatgta
     1141 tatccgtgac catcacggcc ccacctggcg acagataaac attcacctgg tcatgaacac
     1201 tctggggata atccgccagt tcatcacccc ataccgtgaa ttctccggct ctgttactca
     1261 gtatcatgta gcgggttatc atgcccgttc ccggctctct ggcacgcccc agccccgtaa
     1321 taaccccggc taatgccgtt tcacggctca ggcgatggtt atcatggtgt ttcagccgtg
     1381 cgtcatattc ctgttccttc cggcgcgctt ccgcttcggc ttcctccctg cgccgctccg
     1441 cttcccgtgc tgacagtttt tctttcagct ctgccattcc cggcgaaatc cacgtattcc
     1501 actgcgtttc aaaggcctga cgacgggcgg gaatgtcccg ttctttcacg gccctgtagg
     1561 tgcggcgaag agattcaatc tgtttctcga gtttccagaa gcggagttgt cttttgcggt
     1621 attccggttc agcccatgtc atcaggggaa gctctgacag gatggacgct accggacggg
     1681 cttttctgag tccggtcatc tctttttcga gaatatcccg ctctttcacc agcgcattcc
     1741 cctcacgttt gatgtcgttt gccttcccgt tcatcgccac gaactccggt gtcatctccc
     1801 atgcgttccc gcattcctgc ggcagtgtgg caatgaattc ccgcagggta tccgctgagg
     1861 cattcgcggc gggaatggtc agattaaggg cttccgctgc acgacgtgcg gcatcgctga
     1921 gttcccgttt ccgcacgttc tcctgtacct ggatgactgc cagccttgtg cgggaaacct
     1981 gtatttccag gttaaggctg ttaatcaggc ggttctgctc accgcgttct gtttccatgc
     2041 cccgtttttc catcgcacag gcagcctttc cgaggtgaag gcccggcgct ttctccagtc
     2101 cctgacgctc gtatgaacga tggtctatct cttcctggta gccggcgttc gcaagcgctc
     2161 tgttcgcatg gtcagcccat gatgcgcgcc acgtctcggc gagtgcccgg tcgttccagt
     2221 ccctgacctt tcctgcgaat cccgtttccc cgacagctct cgtggtcagc atgatgtgtg
     2281 catgggggtt ggtccggtcc atatgatgga acgccacatc ggcaatcatg ccccgactga
     2341 caaagttttc ccggacaaaa gcgagaacgg cctcccgtgc ggcctcgcgg gaaatctcac
     2401 ggggaatggc gagttcaatc tcccttgcca gctgggagtt ccggcgctgt tcggctttct
     2461 cgaccgcatt ccagagaacg gaacggtcac cacaccagga cggtgcattc acaggggtga
     2521 gaatgaccgc atcatcaacg ccgcgtttac gggtgtaatc gtgggttaat ccggtacggt
     2581 catcgggtat gacagagccg gaacggtagg cagcagaagc aacggcactg tagccgtttt
     2641 ttcgcgaaat gattttcatg ctgagatgat aaatcgccat ttctgccgta atgccttttt
     2701 gccgttttct tttagcgtcg cagaccgcac acaatcgaaa cgaagtgaag attgtataag
     2761 tgcgcacttc gtgatgtgcc gtgcattatg ccagctcagt ttttaaacta ccagtgacgc
     2821 gctaaaatgc gatttttcat cgcgcacgga gttacatcat gagcagaacg ctcgaacaga
     2881 agattgctga agctgaggcc agattgcagc gcctgaaggc gaagagccgg agcctggaca
     2941 ctgcgcaaaa agtcattgtg ggagcagcca tgctggcgag ggtacggagg ccggaagagg
     3001 cgcaactgcg tgcgttcctg ctccagttcc tgcgaaagga agtcacaaga caggccgatg
     3061 tgaaccggct acaaccactg attaacgagc tggagaagct accaagacca cctgcgaaac
     3121 cgcagaacgg ataagccccg gcgcgtaagt gccacatgca ccaccggacg cctttgcgct
     3181 tcctcgcaca ttcgctcgct acgctcggtc atgaggctgc ggcgagcgct accaccgcaa
     3241 tcacgaggaa accagcgcca ttgctgggcg gaaccggaaa aaccgcagga acgccaacag
     3301 ctcaaaaaag cgccgaaaag gcgctgttat ctgataaggc tatttgtgca ttgcccaatt
     3361 acggatcgta tttcgatgta catccagcat cgccgcaata gctttctgag aatatccatt
     3421 ctccagcata catagcgcca tgaaacgctt gtcctcgtag gcttcgcctt tagcaaggcc
     3481 acctttccgg cctcgagcgg cctgtacagc ggaaaagcct tccggtgaga attttctgtg
     3541 cgtgtatttc gcaatgctct tgccaatagc ccggcattca gccagtgaaa gaggaacggg
     3601 aagcgatgcg ttgtacattt cgacacgctg gatcacggca tcaagccact gtgagaatgc
     3661 tggccatccc tgacgaatcg ctctgtaagc ccatttacgc gttatttcga acaggtggca
     3721 gtttcgcccc agcccgtaat gtttatcgac gctacgacgc tctgaggcgc tcaaatcgag
     3781 ataatcagcc agttcatcga gggtataggc ttcctcgcgc cactccatca cctgccattc
     3841 caggtggaac ggatttttgc aaatcagtcc gctgtagttc acatctgcgt caagtttctc
     3901 acacagcgca cgttcaattg cagcggcgta tttcagcacc ttaaccgacg catcaggcgc
     3961 ggttctcacg gcaagattga gcgcgtatag caggtgagcg tgcccattca cgggattttt
     4021 tacggtgatg ttcggcgcgg gggcgttccg gtcgctccag tcaatcgcag ccccctcgcg
     4081 gtcaacgtca aaaaccagcc agtgttgcgc atgtggctgg ttctgctgaa tgtaccgcgc
     4141 aagaagcgca cgccctttgc cggagatgcg aaggccgaaa gcgggatcat ccgtgtgata
     4201 gggacggtga ggtaaatttt cttcgaagta ttga
//
