LOCUS       NZ_CP080176             3553 bp    DNA     circular CON 17-FEB-2024
DEFINITION  Escherichia coli strain PK8566 plasmid pPK8566-3kb, complete
            sequence.
ACCESSION   NZ_CP080176
VERSION     NZ_CP080176.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN20353536
            Assembly: GCF_019428785.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3553)
  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 3553)
  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 08:12:03
            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)                     :: 5,195
            CDSs (total)                      :: 5,078
            Genes (coding)                    :: 4,771
            CDSs (with protein)               :: 4,771
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 85
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 307
            CDSs (without protein)            :: 307
            Pseudo Genes (ambiguous residues) :: 0 of 307
            Pseudo Genes (frameshifted)       :: 108 of 307
            Pseudo Genes (incomplete)         :: 209 of 307
            Pseudo Genes (internal stop)      :: 63 of 307
            Pseudo Genes (multiple problems)  :: 63 of 307
            Pseudo Genes (short protein)      :: 2 of 307
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP080176.1.
            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..3553
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PK8566"
                     /isolation_source="chicken"
                     /db_xref="taxon:562"
                     /plasmid="pPK8566-3kb"
                     /geo_loc_name="Pakistan: Faisalabad"
                     /lat_lon="31.40 N 73.13 E"
                     /collection_date="2020-04-11"
                     /collected_by="Mashkoor Mohsin"
     gene            complement(176..901)
                     /locus_tag="KZY09_RS25705"
                     /old_locus_tag="KZY09_25660"
     CDS             complement(176..901)
                     /locus_tag="KZY09_RS25705"
                     /old_locus_tag="KZY09_25660"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001307201.1"
                     /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_001427890.1"
                     /translation="MASMETEQQPQQTTEQIEVKTKRVQCFIDGYNLYHAIEETGNKAL
                     HWVDLKSLCKRYLPKNASIDNVFWFSAKPSHLSRAINENYQNYTNALTECGVDVIGGRF
                     KKKNVTCEADNGCGGVFHKHEEKESDVNLAISLVSGACNDEYDIAIIITADSDLCPPIK
                     YVRERFPNKELWLVAPPGRIRRATDLCSLSSRSMEIKNDALRACCMRDEFYKDGVLVAR
                     RPQEWRAVANTRQRRARSR"
                     /name="NYN domain-containing protein"
     gene            1221..1835
                     /locus_tag="KZY09_RS25710"
                     /old_locus_tag="KZY09_25665"
     CDS             1221..1835
                     /locus_tag="KZY09_RS25710"
                     /old_locus_tag="KZY09_25665"
                     /inference="COORDINATES: protein motif:HMM:NF025107.4"
                     /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_052895292.1"
                     /translation="MSTKNAQKEQKKESLITTHWGDDATIHGWTAIPNSLLMLQGDLGI
                     GSTEMCILLNILMHQWPESGESISFPSIGTIASRIGVSKRTIQRGVSNLEALGILTRYQ
                     STRNDPLTNGANIFDSTPLKEYLNKKAKGITISNSNKKKERKKTGITPNIKLPRICPKC
                     LKTKATSHEEIVKFFGVRKTMAGEIINSYCKECRASEKDLF"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(2122..2445)
                     /gene="mobA"
                     /locus_tag="KZY09_RS25715"
                     /old_locus_tag="KZY09_25670"
     CDS             complement(2122..2445)
                     /gene="mobA"
                     /locus_tag="KZY09_RS25715"
                     /old_locus_tag="KZY09_25670"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            2729..2923
                     /locus_tag="KZY09_RS25720"
                     /old_locus_tag="KZY09_25675"
     CDS             2729..2923
                     /locus_tag="KZY09_RS25720"
                     /old_locus_tag="KZY09_25675"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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_001041640.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3411..3524
                     /locus_tag="KZY09_RS26370"
     CDS             3411..3524
                     /locus_tag="KZY09_RS26370"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001712890.1"
                     /translation="MHEPPVQPDRCALSGNYRLESNPERHDLTPLAAAIGN"
                     /name="hypothetical protein"
     Typing          complement(2455..2694)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          2959..3480
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.437"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          complement(2126..2445)
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="2.86e-62"
ORIGIN
        1 acctgataag gctaaactga aagaacaagt tttggcgact gtgctcctca aagccagtta
       61 cctcggttca aagagcgcca actctatgaa ccttcgaaaa accgcccgcc aaggcggttt
      121 tttcgttttc aacctagtta gattaatctc cttgcgctag ctgcgtcaac aaagcctaac
      181 gacttctagc ccttctttgc ctggtattgg caacagctcg ccattcctga ggccttctgg
      241 ctacaagtac tccatctttg tagaactcat cacgcataca gcaggctctc aaagcatcat
      301 tcttgatctc catacttctc gatgacagag agcagagatc tgtcgctcgc ctgattctcc
      361 ccggaggagc tacaagccaa agctctttat tagggaatcg ctctcttacg tatttaatag
      421 gggggcataa gtcagaatcc gcagtgataa taatggctat atcatactca tcattacacg
      481 caccagacac tagacttata gccaaattaa catcggactc tttttcttca tgcttatgga
      541 aaactccacc acatccatta tcagcttcgc acgttacatt ctttttttta aaacgcccac
      601 cgataacatc aacaccacat tcggttaaag cgttggtgta attttgataa ttttcattta
      661 tggctcttga taaatgtgat ggcttagcgg aaaaccaaaa aacattatca atagatgcat
      721 ttttaggaag gtatctcttg cataaagatt taagatcaac ccaatgaaga gctttattac
      781 cagtctcttc aattgcatga tataaattat acccatcaat aaagcactgc actcgctttg
      841 tttttacttc gatttgctca gtagtttgtt gtggttgctg ctctgtttcc atacttgcca
      901 tttttgacct ctagatagca aaaaggcctg catatgcagg cctttttgcg tctcttaacc
      961 gcagttaaca gaccactgta tggacgcatc caatacagga agaattttgt acaatgcgct
     1021 tccaagcctc gacttggata gccactaaga gcataactct taggtagtgg actcaactta
     1081 agttctatat aaaaaaagag caaatggatg acatttatgt catcctaaaa gatacatgtt
     1141 actacctaac tactcttata ttaagagtag ttaggtagta actgttcaca tttgattttt
     1201 ttttcgcgag aaaagcatct atgagcacaa aaaacgcaca gaaagaacaa aaaaaagagt
     1261 cattaatcac tactcactgg ggagatgatg caaccataca tgggtggacg gctataccaa
     1321 atagcctcct tatgctgcaa ggtgatcttg gtattgggag tactgagatg tgtattctgc
     1381 tgaatatatt gatgcatcaa tggcctgagt caggggagtc aatatctttt ccgtcaattg
     1441 gtaccattgc atcaagaata ggtgtatcta aaagaacaat tcaacgcggg gttagtaacc
     1501 tagaggcatt ggggatatta actagatacc aatcaacaag gaatgaccct ctaaccaatg
     1561 gcgctaatat attcgactca actcctctaa aagaatattt aaacaaaaaa gctaaaggca
     1621 taacaattag caacagcaac aaaaagaaag aaagaaagaa aaccggaatt acacccaaca
     1681 taaaattacc acgcatttgc ccaaaatgtt tgaaaactaa agcaaccagc cacgaagaaa
     1741 ttgttaaatt ttttggcgtg cgaaaaacaa tggctgggga aataataaat tcatattgca
     1801 aagaatgccg agcttctgaa aaagatctat tttaaacagt tgaccatttt ttatatggcc
     1861 aactgccccc actcaagtaa atgggactgt ttctaacgct cccatttacc ataacgtctc
     1921 attacgcgca ccgctaaaac gcgctgaacg cgattctgcc gcaaacaccg caaaaagaga
     1981 tgttttcccc ggggtaaacc ggaaaaatgc gtcaggattg ctttcagctc actgcatagc
     2041 tatgcatgaa agtgaatggc gatcggtttg gggacttacg gcgttcatac cgtctgtttt
     2101 cgacagtttc cctccgggaa gctaatctgc cataagcctg gataacaggg cccggtgata
     2161 ctccgtaata gctatcagca cctccgcata ctctctgtcc ccgacacgct tgccgtcgat
     2221 aaagagtttt ttctgcaacg cccccagtcg catgacttct ttcagcactc ggtcatcagt
     2281 cagtgaatta actttcttac cgagagctgc cgcccgtaaa aaaccagaaa cggtcttgcc
     2341 gcattcagca gccctttttc tgatttcctg gtcttcttct gccgtcagac gaacagggcg
     2401 actgatagcc cgcctgcgcg tattacttcc acttcgtttt gtcataaaac atggctccgt
     2461 atctgacatg ggtgtcgggg caaagccctg accagggtaa ttgtaatagc gtgcatgtat
     2521 gcgcggtata acaattgcac atcctgtcct gtcagcaagc tcgaattacc gacaaaagca
     2581 cggcagtttt ttggcagtga cagtgttgtc tgacagaaat gcccgtcaaa gagtcagaca
     2641 gcagaatacc ggcggtaaaa cagtcgaaaa gtggtactcg atataatcac acaacgcaga
     2701 tgacagaaag aacggagaaa acagaaagat gaacaagcag cagcaaaccg tactcaacat
     2761 ggcgggattc ataaaaagcc agagcctgac gctgctcgaa aaactggacg cacttgatgc
     2821 tgacgaacag gccgccatgt gtgagaagct gcacgaactc gcggaagaac ttcagaacag
     2881 catacagaca cgctttgaag cggaaaatcg caccgggata taacgcaccc ggacaggatg
     2941 cagaacggca tagcggagcg taaggagaaa atgccacgtc agacgctctt ccgcttcctc
     3001 gctcactgac tcgctacgct cggtcgttcg actgcggcga gcggtgtcag ctcactcaaa
     3061 ggcggtaata cggttatcca cagaatcagg ggataacgcc ggaaagaaca tgtgagcaaa
     3121 aagcaaagca ccggaacaag ccagcgccga tgccgttttt ccataggctc cgcccccctg
     3181 acgagcatca caaaaatcga cgctcaagtc agaggtggcg aaacccgaca ggactataaa
     3241 gataccaggc gtttccccct ggaagctccc tcgtgcgctc tcctgttccg accctgccgc
     3301 ttaccggata cctgtccgcc tttctccctt cgggaagcgt ggcgctttct catagctcac
     3361 gctgttggta tctcagttcg gtgtaggtcg ttcgctccaa gctgggctgt gtgcacgaac
     3421 cccccgttca gcccgaccgc tgcgccttat ccggtaacta tcgtcttgag tccaacccgg
     3481 aaagacacga cttaacgcca ctggcagcag ccattggtaa ctgatttaga ggagttgagt
     3541 cttgaagtta tgc
//
