LOCUS       NZ_CP080169             4234 bp    DNA     circular CON 17-FEB-2024
DEFINITION  Escherichia coli strain PK8275 plasmid pPK8275-4kb, complete
            sequence.
ACCESSION   NZ_CP080169
VERSION     NZ_CP080169.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN20353479
            Assembly: GCF_019428765.1
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 08:27:08
            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)                     :: 5,648
            CDSs (total)                      :: 5,529
            Genes (coding)                    :: 5,219
            CDSs (with protein)               :: 5,219
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 89
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 310
            CDSs (without protein)            :: 310
            Pseudo Genes (ambiguous residues) :: 0 of 310
            Pseudo Genes (frameshifted)       :: 126 of 310
            Pseudo Genes (incomplete)         :: 212 of 310
            Pseudo Genes (internal stop)      :: 61 of 310
            Pseudo Genes (multiple problems)  :: 78 of 310
            Pseudo Genes (short protein)      :: 5 of 310
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP080169.1.
            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="PK8275"
                     /isolation_source="chicken"
                     /db_xref="taxon:562"
                     /plasmid="pPK8275-4kb"
                     /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(2777..4234,1..762))
                     /gene="mobQ"
                     /locus_tag="KZY08_RS27955"
                     /old_locus_tag="KZY08_27975"
     CDS             complement(join(2777..4234,1..762))
                     /gene="mobQ"
                     /locus_tag="KZY08_RS27955"
                     /old_locus_tag="KZY08_27975"
                     /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            941..1216
                     /locus_tag="KZY08_RS27960"
                     /old_locus_tag="KZY08_27980"
     CDS             941..1216
                     /locus_tag="KZY08_RS27960"
                     /old_locus_tag="KZY08_27980"
                     /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"
     gene            complement(1422..2330)
                     /locus_tag="KZY08_RS27965"
                     /old_locus_tag="KZY08_27985"
     CDS             complement(1422..2330)
                     /locus_tag="KZY08_RS27965"
                     /old_locus_tag="KZY08_27985"
                     /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"
     Typing          405..763
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.444"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          764..934
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="97.674"
                     /coverage="98.0"
                     /evalue="5.58e-78"
     Typing          complement(1603..2330)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.376"
                     /coverage="94.0"
                     /evalue="0.0"
     Typing          complement(2..762)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.457"
                     /coverage="100.0"
                     /evalue="5.26e-159"
ORIGIN
        1 gagttcccgt ttccgcacgt tctcctgtac ctggatgact gccagccttg tgcgggaaac
       61 ctgtatttcc aggttaaggc tgttaatcag gcggttctgc tcaccgcgtt ctgtttccat
      121 gccccgtttt tccatcgcac aggcagcctt tccgaggtga aggcccggcg ctttctccag
      181 tccctgacgc tcgtatgaac gatggtctat ctcttcctgg tagccggcgt tcgcaagcgc
      241 tctgttcgca tggtcagccc atgatgcgcg ccacgtctcg gcgagtgccc ggtcgttcca
      301 gtccctgacc tttcctgcga atcccgtttc cccgacagct ctcgtggtca gcatgatgtg
      361 tgcatggggg ttggtccggt ccatatgatg gaacgccaca tcggcaatca tgccccgact
      421 gacaaagttt tcccggacaa aagcgagaac ggcctcccgt gcggcctcgc gggaaatctc
      481 acggggaatg gcgagttcaa tctcccttgc cagctgggag ttccggcgct gttcggcttt
      541 ctcgaccgca ttccagagaa cggaacggtc accacaccag gacggtgcat tcacaggggt
      601 gagaatgacc gcatcatcaa cgccgcgttt acgggtgtaa tcgtgggtta atccggtacg
      661 gtcatcgggt atgacagagc cggaacggta ggcagcagaa gcaacggcac tgtagccgtt
      721 ttttcgcgaa atgattttca tgctgagatg ataaatcgcc atttctgccg taatgccttt
      781 ttgccgtttt cttttagcgt cgcagaccgc acacaatcga aacgaagtga agattgtata
      841 agtgcgcact tcgtgatgtg ccgtgcatta tgccagctca gtttttaaac taccagtgac
      901 gcgctaaaat gcgatttttc atcgcgcacg gagttacatc atgagcagaa cgctcgaaca
      961 gaagattgct gaagctgagg ccagattgca gcgcctgaag gcgaagagcc ggagcctgga
     1021 cactgcgcaa aaagtcattg tgggagcagc catgctggcg agggtacgga ggccggaaga
     1081 ggcgcaactg cgtgcgttcc tgctccagtt cctgcgaaag gaagtcacaa gacaggccga
     1141 tgtgaaccgg ctacaaccac tgattaacga gctggagaag ctaccaagac cacctgcgaa
     1201 accgcagaac ggataagccc cggcgcgtaa gtgccacatg caccaccgga cgcctttgcg
     1261 cttcctcgca cattcgctcg ctacgctcgg tcatgaggct gcggcgagcg ctaccaccgc
     1321 aatcacgagg aaaccagcgc cattgctggg cggaaccgga aaaaccgcag gaacgccaac
     1381 agctcaaaaa agcgccgaaa aggcgctgtt atctgataag gctatttgtg cattgcccaa
     1441 ttacggatcg tatttcgatg tacatccagc atcgccgcaa tagctttctg agaatatcca
     1501 ttctccagca tacatagcgc catgaaacgc ttgtcctcgt aggcttcgcc tttagcaagg
     1561 ccacctttcc ggcctcgagc ggcctgtaca gcggaaaagc cttccggtga gaattttctg
     1621 tgcgtgtatt tcgcaatgct cttgccaata gcccggcatt cagccagtga aagaggaacg
     1681 ggaagcgatg cgttgtacat ttcgacacgc tggatcacgg catcaagcca ctgtgagaat
     1741 gctggccatc cctgacgaat cgctctgtaa gcccatttac gcgttatttc gaacaggtgg
     1801 cagtttcgcc ccagcccgta atgtttatcg acgctacgac gctctgaggc gctcaaatcg
     1861 agataatcag ccagttcatc gagggtatag gcttcctcgc gccactccat cacctgccat
     1921 tccaggtgga acggattttt gcaaatcagt ccgctgtagt tcacatctgc gtcaagtttc
     1981 tcacacagcg cacgttcaat tgcagcggcg tatttcagca ccttaaccga cgcatcaggc
     2041 gcggttctca cggcaagatt gagcgcgtat agcaggtgag cgtgcccatt cacgggattt
     2101 tttacggtga tgttcggcgc gggggcgttc cggtcgctcc agtcaatcgc agccccctcg
     2161 cggtcaacgt caaaaaccag ccagtgttgc gcatgtggct ggttctgctg aatgtaccgc
     2221 gcaagaagcg cacgcccttt gccggagatg cgaaggccga aagcgggatc atccgtgtga
     2281 tagggacggt gaggtaaatt ttcttcgaag tattgaagcg cggcgctcat gtgttacgat
     2341 tccttccagg ttatcgaccg acatcgcccc tgtatcttcg tgaaagtctt ggcggatcta
     2401 cacgaatttc aggggcgttt gtttttcagt cgcttacact acacccaacg gcaaatcctg
     2461 tcgatccttc ccgaaaaacc gatccattta ccataactcc tgttgtacgt accccttaaa
     2521 acgctctcag acgcgttctg acgcaaaaaa cgcaaaaaga caaggaaaca ccagggtaaa
     2581 ccagaaaaac gcgtcagaat cgttttcagg agcctgcata actatgcacg aaagcaatgc
     2641 gcgatcggtt tcgaccgttc agaagcgcga acgggtcaaa acggcaaact ttctcatcca
     2701 gaaaacgcct cacgggacgc ggaatttttt cgtgtcccgt gagacgttgg cggggttcgg
     2761 ggtgcagccc cggatatcac atactcatgc cccggtaatg tccggggcgt cgttgttgtt
     2821 gcctgtgctg ttcgtcccgc ttccattcat gccaggtctg attaaatccg agttgacgga
     2881 agagataatc cggcatctct tccggtttgt tgatggcagc aaaaagcgtg tcctgacagc
     2941 ccttaagcct gaactgcatc agcttcggtt ccggtgggta cggagtatca gcatcacggt
     3001 ttatggcctc accgtagcct gccaggtgta tcccgttctc tgtgatgatg cttaccatca
     3061 gatgactgta atccggcgac ggaagcgcaa gaacgggacg cagctcgtcc tccaggcgca
     3121 caaaaccgac aagcatttcc tccggccctt tgcacaacag cagattcagc gtcctgctgt
     3181 ttcgctctgt cgaaaagaca acgggcatga gttgctccgg tgccgcataa gcggtgacgt
     3241 ccacccggtg cgctgacggc agcggagagg ctgcgggcct gcggtcatcg ctgaaataaa
     3301 aattatccgg ccagtgatgc ggcagcgccg gaaaaccgta agagggccac ccctggcgca
     3361 tctgttccag tacatgccgg accgtcgcac cggaatacat tctcacacgc tcaggccggg
     3421 ccagcgtctc atgagattct gacagccccg aatgtatatc cgtgaccatc acggccccac
     3481 ctggcgacag ataaacattc acctggtcat gaacactctg gggataatcc gccagttcat
     3541 caccccatac cgtgaattct ccggctctgt tactcagtat catgtagcgg gttatcatgc
     3601 ccgttcccgg ctctctggca cgccccagcc ccgtaataac cccggctaat gccgtttcac
     3661 ggctcaggcg atggttatca tggtgtttca gccgtgcgtc atattcctgt tccttccggc
     3721 gcgcttccgc ttcggcttcc tccctgcgcc gctccgcttc ccgtgctgac agtttttctt
     3781 tcagctctgc cattcccggc gaaatccacg tattccactg cgtttcaaag gcctgacgac
     3841 gggcgggaat gtcccgttct ttcacggccc tgtaggtgcg gcgaagagat tcaatctgtt
     3901 tctcgagttt ccagaagcgg agttgtcttt tgcggtattc cggttcagcc catgtcatca
     3961 ggggaagctc tgacaggatg gacgctaccg gacgggcttt tctgagtccg gtcatctctt
     4021 tttcgagaat atcccgctct ttcaccagcg cattcccctc acgtttgatg tcgtttgcct
     4081 tcccgttcat cgccacgaac tccggtgtca tctcccatgc gttcccgcat tcctgcggca
     4141 gtgtggcaat gaattcccgc agggtatccg ctgaggcatt cgcggcggga atggtcagat
     4201 taagggcttc cgctgcacga cgtgcggcat cgct
//
