LOCUS       NZ_CP080153             3852 bp    DNA     circular CON 17-FEB-2024
DEFINITION  Escherichia coli strain PK8276 plasmid pPK8276-3kb, complete
            sequence.
ACCESSION   NZ_CP080153
VERSION     NZ_CP080153.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN20353404
            Assembly: GCF_019428725.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3852)
  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 3852)
  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 08:09:27
            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)                     :: 5,272
            CDSs (total)                      :: 5,154
            Genes (coding)                    :: 4,770
            CDSs (with protein)               :: 4,770
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 8
            Pseudo Genes (total)              :: 384
            CDSs (without protein)            :: 384
            Pseudo Genes (ambiguous residues) :: 0 of 384
            Pseudo Genes (frameshifted)       :: 174 of 384
            Pseudo Genes (incomplete)         :: 232 of 384
            Pseudo Genes (internal stop)      :: 64 of 384
            Pseudo Genes (multiple problems)  :: 79 of 384
            Pseudo Genes (short protein)      :: 5 of 384
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP080153.1.
            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..3852
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PK8276"
                     /isolation_source="chicken"
                     /db_xref="taxon:562"
                     /plasmid="pPK8276-3kb"
                     /geo_loc_name="Pakistan: Faisalabad"
                     /lat_lon="31.44 N 73.07 E"
                     /collection_date="2020-10-20"
                     /collected_by="Mashkoor Mohsin"
     gene            complement(join(2955..3852,1..122))
                     /locus_tag="KZY06_RS26140"
                     /old_locus_tag="KZY06_26125"
     CDS             complement(join(2955..3852,1..122))
                     /locus_tag="KZY06_RS26140"
                     /old_locus_tag="KZY06_26125"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001271372.1"
                     /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_130568422.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWLVMEWREEAYTLDELADYLDLSASA
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLDAVIQRVEMYNASLPVPLSP
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKANSSANQSDKGKKS
                     AAVRWTANDDKRRRALDMYILGASTEDIAEAVGVSRWTVRRWMDSSVEWLLSKQIIKI"
                     /name="replication initiation protein"
     gene            complement(555..1085)
                     /locus_tag="KZY06_RS26145"
                     /old_locus_tag="KZY06_26130"
     CDS             complement(555..1085)
                     /locus_tag="KZY06_RS26145"
                     /old_locus_tag="KZY06_26130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000168768.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000168766.1"
                     /translation="MASTEEGLLTLLLSVEHLKNTAIEQQKAVADTLAVARETLRGYRD
                     ISDSVVKQVSDEVRKGVQKTDIAGLMGERMTQDFQRLEETVAKMRANAEALNKDIATIH
                     HNVVKEYNTLNKYSLKWFIGVTVSFLVMFSLLGWFTKTLIDRNYTATEVVYQKIVDIEK
                     KLDKPATGKSRKN"
                     /name="hypothetical protein"
     gene            complement(1097..2050)
                     /locus_tag="KZY06_RS26150"
                     /old_locus_tag="KZY06_26135"
     CDS             complement(1097..2050)
                     /locus_tag="KZY06_RS26150"
                     /old_locus_tag="KZY06_26135"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016235474.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="WP_001360358.1"
                     /translation="MATYHLNVKFGGKGQAGNHADYIERKGEYEKRKDLEYSEHGNMPG
                     WARDNPSHFWQAADQFERANGSTYREIEIALPRELTPDQRIELVQDFVRQVAGERHAYS
                     FAIHNPKASIDGGEQPHAHIMMSQRINDGMERSPEQYFRRYNAKNPERGGAKKDSGNLT
                     PTQQKEQLRTLRASWSALQNEHLARHGHRVRVDHRSLEERGIKRTPERHFGFAASSRLD
                     HAQRREILQNRAQPLEHFLEKAHSVRHQFDAQVQQKELVKTLLQDVARERGHALTARIN
                     KTGEVEFERAPTRTRSNTRGHGMGIRDNSRGYDYER"
                     /name="MobA/MobL family protein"
     gene            2230..2625
                     /locus_tag="KZY06_RS26155"
                     /old_locus_tag="KZY06_26140"
     CDS             2230..2625
                     /locus_tag="KZY06_RS26155"
                     /old_locus_tag="KZY06_26140"
                     /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_095462619.1"
                     /translation="MRISNIDWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNELQAQENARKQANQKRMEGKTQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELRYPKDKILQRLKVVRHDLETSPDHN"
                     /name="hypothetical protein"
     Typing          complement(3199..3852)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="98.168"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(1101..2050)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.685"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tggatgtacc gcgcaagaag cgcacgccct ttgccggaga tgcgaaggcc gaaagcgaga
       61 tcatccgtgt gatagggacg gtgaggtaaa ttttcttcga agtattgaag cgcggcgctc
      121 atgtgttacg attccttcca ggttatcgac cgacctcgcc cctgtattct cgtgacaatc
      181 ttggcggaga gacacgaatt tcaggggcgt ttgtttttca gtcgcttaca ctacccccaa
      241 caacaaaacc tgtcgagcct tcccgcaaaa ccgatccatt taccataact cccgttgcgc
      301 gcaccgctaa aacgccctca gtcgcttcct gacgcaaaaa acgcaaaaag acaggaaaac
      361 accaggccaa accagaaaaa cgcgtcagaa tcgttttcag agcgttgcat aactatgcac
      421 gaaagcgatg cgcgatctgt ttcgagcgtt cagaagggcg aacgggtcaa aacagcaaac
      481 tttctcatca gaaaacggtg aacgggacgc ggaatttttt cgcgttccgt gaggcgttgg
      541 acaagcgaag cgcgtcagtt tttccggctc ttccctgttg ctggtttgtc cagtttcttt
      601 tcaatatcaa caattttctg atacacgacc tccgtcgcgg tgtagttcct gtcgatcaac
      661 gttttggtaa accagccaag caacgagaac atgaccagaa aactgaccgt aacaccgata
      721 aaccatttca gactgtattt attgagcgtg ttgtattctt taacaacatt gtgatgaatt
      781 gtcgcaatgt ccttgttaag cgcctccgcg ttggctctca tctttgccac agtctcttca
      841 agacgctgaa aatcctgggt catgcgctca cccatcagcc ccgcaatgtc cgttttctgt
      901 accccttttc tgacttcatc gctaacctgt tttacaacac tgtcagaaat atcccgatac
      961 ccccgcagtg tttcccttgc gaccgccagc gtgtctgcaa ccgctttctg ttgttctatc
     1021 gcagtgtttt tcaaatgctc aacggacaac aagagcgtga gcaacccctc ttctgtactc
     1081 gccatacagt ccccttttaa cgttcgtagt cgtacccgcg tgagttgtca cgaatgccca
     1141 tgccgtgccc tcgcgtgtta ctccgcgtcc gcgttggcgc acgttcaaat tcaacttcac
     1201 ctgttttatt tattcttgcc gtaagcgcgt gccctcgctc ccgtgcgacg tcctgtaaaa
     1261 gcgttttaac taactctttt tgctgaactt gtgcatcaaa ttgatggcga accgaatgcg
     1321 ctttctctag aaaatgttcg agcggctgcg ctcggttttg caggatttcg cggcgctgcg
     1381 catgatcaag ccgtgatgag gcggcaaatc cgaaatgccg ttctggcgtg cgtttaattc
     1441 cgcgttcttc cagtgagcga tggtcaacgc gcaccctgtg accatgacgc gctaaatgct
     1501 cgttctgtaa cgctgaccag ctcgcccgta acgtccgcaa ttgctctttt tgctgagtcg
     1561 gtgtcagatt gcctgaatct ttttttgcgc ctccccgttc gggattcttg gcgttataac
     1621 gccggaaata ctgttccggc gaacgttcca taccatcgtt aatacgctgg ctcatcatga
     1681 tatgcgcatg aggctgttcc cctccgtcaa tgctcgcttt tggattgtga atggcaaagc
     1741 tataggcgtg ccgttctcca gctacctgac gcacaaaatc ctgcaccagt tcaatgcgct
     1801 gatccggtgt cagttcacgc ggcaaggcga tttcgatctc ccgataagtc gaaccattcg
     1861 cacgttcaaa ctgatcagcc gcttgccaga aatgggaggg attatctcgc gcccagcctg
     1921 gcatattccc gtgctctgag tattccagat cttttcgttt ctcgtactcg cctttgcgtt
     1981 cgatgtaatc ggcatggttt ccggcctgtc ccttgccgcc aaattttaca ttgaggtgat
     2041 aggttgccac ggtgttagcc ctccgcagga gcgcacatgt ttctgagcca acggcgaaga
     2101 aacatataag tgcgcttcct gctaatttta cgaattagca cggaagatac tcccctgcac
     2161 ccacccaccg caagcgatat actgcacaac cacaacacac cgcaaaaaac accagggagc
     2221 atcccaaaca tgcgcatcag caacatcgac tggttgaaga aacgaatcgg ctttatcagg
     2281 aagctcggag aacagaccgc acgacagagg cagatcattg acctgctcga caacgaagcc
     2341 ggactaacag aacaggagcg caaactactc cacgtcctgg caaccgcaga aaaaaacgag
     2401 ctacaggcac aggagaacgc acgcaaacag gccaaccaaa aacggatgga ggggaaaaca
     2461 caacgacggg aacgcaatca ccgcctgttc cttgcggcgg ggttactgat cgaggccgga
     2521 ctagtggaca caaaaacagg cgaactaaga tacccaaaag acaagatatt acaaagactt
     2581 aaagtggtca ggcacgatct ggaaacaagc cctgatcata attaatttcg aaacgaaaat
     2641 ttcgcgacgc gtatacgcgc gaggggggct ttggtgcgta agtgctcaat gtgacttccg
     2701 gttatcttcc gcttcctcgc ccactcgcga gcctggcggc tcggtcgcta gggctgcggc
     2761 gagcggagcc gccactcgcg tggtttgcag ggtttcggta tttggtttgg gggtgtagga
     2821 gcgggtcgga aacaccgcgc aaaaaaaaca ccaaaccccc gctcaggcgc tgttatctga
     2881 tataggcttg ttcatgcacc caaaattaac aaaaaactaa caaaaaaggg ggggttatgt
     2941 tttctttttg ttaattatat tttaattatt tgtttactta gtagccattc tacagagcta
     3001 tccatccagc gtcgaacagt ccaacggcta acaccaaccg cctctgcaat atcttctgtt
     3061 gaggctccca agatgtacat atcaagcgcc ctacgacgct tgtcatcgtt agcagtccat
     3121 cgaacagcgg cgcttttttt ccctttgtcc gactgatttg ctgatgaatt ggccttaccg
     3181 cccttgcgac ctcgtgcggc ctgaatttct ggcgtgtgcg tatcagccac atactgtgcg
     3241 aaagtttccg gcgtgaagtt cctgtgcgtg tatttcgcaa tgctcttgcc aatagcccga
     3301 cattcagccg gtgaaagcgg aacgggaagc gatgcgttat acatttcgac acgctggatc
     3361 acggcatcaa gccactgtga gaatgctggc cagccctgac gaatcgccct gtaagcccat
     3421 ttgcgcgtca tttcgaacag gtggcagttt cgccccatcc cataatgttt atcgatgcta
     3481 cgacgcgctg aggcgctcaa atcgagataa tcagccagtt catcgagggt ataggcttcc
     3541 tcgcgccact ccatcaccag ccattccagg tggaacggat ttttgcaaat caggccgctg
     3601 tagttcacat ccgcacaaag tttctcacac agcgaacgtt caaccgctgc ggcatatttc
     3661 agcgccttaa ccgacgcatc aggcgcggtt ctcacggcga tattgagtgc atagagcagg
     3721 tgagcgtgtc cgttcacagg atttttaacg gtgatgttcg gcgcgggggc gttccggtcg
     3781 ctccagtcaa tcgctgcccc ctcgcggtca acgtcaaaaa ccagccagaa ctgcgcatgt
     3841 ggctggttct gc
//
