LOCUS       NZ_CP080144             5304 bp    DNA     circular CON 17-FEB-2024
DEFINITION  Escherichia coli strain PK8241 plasmid pPK8241-5kb, complete
            sequence.
ACCESSION   NZ_CP080144
VERSION     NZ_CP080144.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN20353352
            Assembly: GCF_019428705.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5304)
  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 5304)
  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 07:59:14
            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)                     :: 5,930
            CDSs (total)                      :: 5,804
            Genes (coding)                    :: 5,446
            CDSs (with protein)               :: 5,446
            Genes (RNA)                       :: 126
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 93
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 358
            CDSs (without protein)            :: 358
            Pseudo Genes (ambiguous residues) :: 0 of 358
            Pseudo Genes (frameshifted)       :: 124 of 358
            Pseudo Genes (incomplete)         :: 234 of 358
            Pseudo Genes (internal stop)      :: 55 of 358
            Pseudo Genes (multiple problems)  :: 51 of 358
            Pseudo Genes (short protein)      :: 4 of 358
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP080144.1.
            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..5304
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="PK8241"
                     /isolation_source="chicken"
                     /db_xref="taxon:562"
                     /plasmid="pPK8241-5kb"
                     /geo_loc_name="Pakistan: Faisalabad"
                     /lat_lon="31.50 N 72.97 E"
                     /collection_date="2020-05-11"
                     /collected_by="Mashkoor Mohsin"
     gene            complement(join(5181..5304,1..137))
                     /locus_tag="KZY05_RS29170"
                     /old_locus_tag="KZY05_29180"
     CDS             complement(join(5181..5304,1..137))
                     /locus_tag="KZY05_RS29170"
                     /old_locus_tag="KZY05_29180"
                     /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="Tn3 family transposase"
                     /protein_id="WP_022650075.1"
                     /translation="MPWDTFAASVTEAQTLARPADFDFLHHIGESYATLRRYAPQFLGV
                     LKLRAAPAAKGVLDAIDMLRGMNSDSARKVPADAPTAFIKD"
                     /name="Tn3 family transposase"
     gene            complement(1334..1525)
                     /locus_tag="KZY05_RS29175"
                     /old_locus_tag="KZY05_29185"
     CDS             complement(1334..1525)
                     /locus_tag="KZY05_RS29175"
                     /old_locus_tag="KZY05_29185"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /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_000165975.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1590..1913
                     /locus_tag="KZY05_RS29180"
                     /old_locus_tag="KZY05_29190"
     CDS             1590..1913
                     /locus_tag="KZY05_RS29180"
                     /old_locus_tag="KZY05_29190"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_000955999.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2122..>2553
                     /locus_tag="KZY05_RS29695"
                     /pseudo=""
     CDS             2122..>2553
                     /locus_tag="KZY05_RS29695"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            2591..3121
                     /locus_tag="KZY05_RS29190"
                     /old_locus_tag="KZY05_29200"
     CDS             2591..3121
                     /locus_tag="KZY05_RS29190"
                     /old_locus_tag="KZY05_29200"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_206353804.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDVHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            3128..3361
                     /locus_tag="KZY05_RS29195"
                     /old_locus_tag="KZY05_29205"
     CDS             3128..3361
                     /locus_tag="KZY05_RS29195"
                     /old_locus_tag="KZY05_29205"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137437.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            <4121..>4216
                     /locus_tag="KZY05_RS29205"
                     /old_locus_tag="KZY05_29215"
                     /pseudo=""
     CDS             <4121..>4216
                     /locus_tag="KZY05_RS29205"
                     /old_locus_tag="KZY05_29215"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013356662.1"
                     /note="incomplete; partial in the middle of a contig;
                     missing N-terminus and C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="amino acid ABC transporter substrate-binding
                     protein"
                     /name="amino acid ABC transporter substrate-binding
                     protein"
     gene            4362..5177
                     /locus_tag="KZY05_RS29210"
                     /old_locus_tag="KZY05_29220"
     CDS             4362..5177
                     /locus_tag="KZY05_RS29210"
                     /old_locus_tag="KZY05_29220"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_032492145.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="aminoglycoside O-phosphotransferase APH(3')-Ia"
                     /protein_id="WP_000018330.1"
                     /translation="MSHIQRETSCSRQRLNSNLDADLYGYKWARDNVGQSGATIYRLYG
                     KPDAPELFLKHGKGSVANDVTDEMVRLNWLTEFMPLPTIKHFIRTPDDAWLLTTAIPGK
                     TAFQVLEEYPDSGENIVDALAAFLRRLHSIPVCNCPFNSDRVFRLAQAQSRMNNGLVDA
                     SDFDDERNGWPVEQVWKEMHKLLPFSPDSVVTHGDFSLDNLIFDEGKLIGCIDVGRVGI
                     ADRYQDLAILWNCLGEFSPSLQKRLFQKYGIDNPDMNKLQFHLMLDEFF"
                     /name="aminoglycoside O-phosphotransferase APH(3')-Ia"
     ARG             4363..5174
                     /name="aph(3')-Ia"
                     /gene="aph(3')-Ia"
                     /gene_name="aminoglycoside O-phosphotransferase APH(3')-Ia"
                     /tool="amrfinderplus"
                     /drug_class="AMINOGLYCOSIDE"
                     /identity="100.0"
                     /coverage="100.0"
     Typing          521..708
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          1904..3465
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 agcacgccca ggaactgcgg cgcgtagcgg cgtagcgtgg catagctttc accgatgtgg
       61 tgcaggaaat caaagtcggc aggccgcgcc aatgtttgcg cttcggtgac gctggcggcg
      121 aaggtgtccc agggcataac ggcctcgagg attgcccccc agcctccatc gataccgtgc
      181 caaatgcacg taaaaaacgg gagcgtttct ggtgtcggaa tgtaaccaag ggggtcagag
      241 gcgcgctaaa acgctctcag gggagtcaaa tagagacgtt tgtaacaaaa agatcaaagg
      301 atcctcttga gatccttttt ttctgcgcgt aatctgctgc ctgtaaacga aaaaaccgcc
      361 ttgcagggcg gtttgatcga aggttaagtc agcttgcaga ctgcttaacc aggtaactgt
      421 cttatgcgag acgagtcacc aaaattgttc ttctagtgta gccgcactcc ggcagccact
      481 tcaagtactc tctaaatatc tcgcacatga cttttaccaa tggctgctgc cagtggcgct
      541 ttgtggtgtc ttttccgggt tggacccaag agaacagtta ccggagaagg cgcagcagtc
      601 gggctgaacg gggggttcct gcatacagcc cagcccggag cgaactgcct aagtcgcccc
      661 gagataccag aagacgtgag ctatgagaaa gcgccacgtg tcccgtaagg gagaaaggcg
      721 gaaaaggtat ccggtaatcg atatggcggg aacgtggggg cgcaggaggg agcgattcac
      781 cggaaacggt gatgatcttt aagccacgtc gggtttcgcc accgctggcg gatttcatgg
      841 ttgagccgca aggctcccac agatgcaccg aaaaagtgtc tgttttgtga agtccgtcag
      901 gggggcggag cctatggaaa aagcgcctcc ggcgcggcct ttcccggggt ttcgtttttt
      961 gcgcacatgt tctttcctgg tttatccccg ggttctgtgg ataacagggt tagcgttttt
     1021 gagaaaggag agtccgctcg ccgcagccga acgaccgagc gtagcgagtc agtgagcgag
     1081 gaagcggaag agcgcctgaa ctggcatttt ctccttacgc atctgtgcgg catttcacac
     1141 cggacatggc gcacttttca tacaatccgc actgaatggt taagccagta tacactccgc
     1201 tatcgctacg tgactgggtc agggcttcgc cccgacaccc caaaggtcaa cggcctgacg
     1261 cgccctggcg ggcttgtctg ctcccggcat ccgctcacag acaagctgtg accgtctccg
     1321 ggagctgcat gtgtcagcgg ttttcaccgt catccccgaa gcgtgcgagg caactgcggt
     1381 aaagctcatc ggcgtggtcg tgaagcgatt cacagatgtc tgcctgttca tccgcgtcca
     1441 gttcgttgag cttctccagc agcgttaatg tctggcctct gatgaagcgg gccatgttaa
     1501 gggcggtttt ttcctgtttg gtcactgatg cctccgtgta agggggggtt ctgttcatgg
     1561 gggtaatgat accgatgaaa cgcgagagga tgctcacgat acgggttact gatgatgaac
     1621 atgcccggtt actggaacgc tgtgagggta aacaactggc ggtatggatg cggcgggtct
     1681 gcctgggtga gccggttgcc cgttccggga agctgccgac actggcaccg ccgttactgc
     1741 gtcagctggc cgccatcggg aataacctta accagacagc gaggaaggtg aacagcgggc
     1801 agtggtcttc cggtgaccgg gttcaggtgg tggccgcact gatggccatc ggggatgagc
     1861 tgcgccggct gcgtctggcg gtcagggaac agggggcgcg ggatgatagt taagtttcat
     1921 gccaggggaa aaggtggtgg cagtggtccg gttgattacc tgctgggaag ggagcgtaac
     1981 cgggaagggg caacggtgct tcaggggaat ccggaagagg tccgggaact catcgatgcc
     2041 acgccatttg cgaagaaata cacgtcaggt gttctgtcgt tcgcggagaa ggagctgccg
     2101 cctggagggc gtgaaaaagt gatggcgagc tttgagcgtg tactgatgcc cggtctcgag
     2161 aaaaatcagt acagcatcct gtgggtggag caccaggaca agggacggct tgagctgaat
     2221 tttgtcattc cgaacatgga gctacagacc ggaaaacgcc tccagccgta ctacgaccgg
     2281 gcagacaggc cgagaattga tgcctggcag acgctggtga atcaccatta cggtctgcat
     2341 gaccccaacg ccccggagaa ccgccggacg ctgacccttc ctgataacct gccggaaacg
     2401 aaacaggcgc ttgctgaggg cgtcacacgc gggatagacg cgctttacca tgccggagag
     2461 ataaaaggcc gtcaggatgt gattcaggcg ctcacagagg cggggcttga agtggtcagg
     2521 gtgacgcgaa gcagtatcag cattgcagac ccgaacggcg ggaggaatat cagactgaaa
     2581 ggagcgtttt atgagcaatc ttttacagac gggcgcggag ttcgagaaaa agctgaaaga
     2641 gagagccgaa tctacagaga aaatgctgaa cgacgagttc aggaagctcg aagaatctgt
     2701 aaacagggaa ctgacctcaa acgaatcttt aatcaggaac gctatcaacg accatacaac
     2761 agccctgaaa gaactgctgg agaggtatca gaaaacgacc gtcgatacga tggacgtgca
     2821 ctggaaaacc gtactgaaaa tgagcgtgaa acgctggctg tggctgatta tcgtctcagt
     2881 actgatgttt gccacgaccg ggagtctgct gtggtaccag ggcatgaaga taaacgcgaa
     2941 tatgaatatt ctccgcgagc agaaagagag tctggagaag ctgaacgcga agacatgggg
     3001 cgtgcgttat cacgaggaca gcaacggacg ttttctggtg ttgccgaagg ggatgaaagc
     3061 cgaaacgaac tggacgaagg acaacggcaa actgaacgca gtgagactgg tgcaggagtg
     3121 acagagcatg acggagctgg aaagacattt gctgaacgca ttagagcaac tgcaacagga
     3181 ctatatgcag cggctgaacg aatgggagaa cgccttcgtg gaattgcaga aaatgttttc
     3241 gcttacgcaa cgggacaacg cgatgctgaa cgggcgagtc atgcagttga gtcagcaggt
     3301 gcagcacttg agcgagcgga cagaacgctt gagccagtta tacagcgaga acaggagata
     3361 agggatgaac ggctgatgca ggaacgcgaa catgagttat ctctggagcg ggagcgtcag
     3421 ccggaaatcc aggagcggac actggatggc ccttcgctgg gatggtgaaa ccatgaaaaa
     3481 tgacgtgttc agtggattaa ggcgggctaa tgtggcctgt agcatctggt tgcataggta
     3541 ttcatgcggt taaaatttat caggtgcgat cgcggcagtt tttcgggtgg tttgttgcca
     3601 tttttacctg tctgctgccg tgatcgcacc gaacgcgttt tggcggtgcg tacaatgcga
     3661 cgttatggta aatggagcgg attttcagga aggagtgata ctaacaactc gaacactgtg
     3721 caaataatga tttttttaaa atatcggtaa cgataataaa ttatttcgtt ttacgccggt
     3781 aataaatata atgtagtttc agtatataaa aaaatatatg aggtgtcttg tgggagcttt
     3841 catgaatctt caacaacgta taaataaact accacaatta tcatccagtt tttcatttgg
     3901 aaaagatatt gataatattc attcatttat ctttaacgaa acttctaaag ataaaattga
     3961 agatttacta agaaaatggg tgtcaggcaa tcagccctgt gtatttggta aattggcaag
     4021 caagaaaatt aaagggcttg atttccattt atctattgta aatagccccc aactatataa
     4081 tgatgatggt catttgtttg attttttgcg taatgaaaga gttcatgcca tgttcctcga
     4141 ctacgaagcg gccaaagatt atgcgacccg ctccaggctg gtcacggcgg cgaatatccc
     4201 ttctttcgga gcgccagaat gatgttggtc tggccggatt ttcatatggc gggaaccacg
     4261 ttgtgtctca aaatctctga tgttacattg cacaagataa aaatatatca tcatgaacaa
     4321 taaaactgtc tgcttacata aacagtaata caaggggtgt tatgagccat attcaacggg
     4381 aaacgtcttg ctcgaggcag cgattaaatt ccaacctgga tgctgattta tatgggtata
     4441 aatgggctcg cgataatgtc gggcaatcag gtgcgacaat ctatcgattg tatgggaagc
     4501 ccgatgcgcc agagttgttt ctgaaacatg gcaaaggtag cgttgccaat gatgttacag
     4561 atgagatggt cagactaaac tggctgacgg aatttatgcc tcttccgacc atcaagcatt
     4621 ttatccgtac tcctgatgat gcatggttac tcaccactgc gatccccggg aaaacagcat
     4681 tccaggtatt agaagaatat cctgattcag gtgaaaatat tgttgatgcg ctggcagcgt
     4741 tcctgcgccg gttgcattcg attcctgttt gtaattgtcc ttttaacagc gatcgcgtat
     4801 ttcgtctcgc tcaggcgcaa tcacgaatga ataacggttt ggttgatgcg agtgattttg
     4861 atgatgagcg taatggctgg cctgttgaac aagtctggaa agaaatgcat aagcttttgc
     4921 cattctcacc ggattcagtc gtcactcatg gtgatttctc acttgataat cttatttttg
     4981 acgaggggaa attaataggt tgtattgatg ttggacgagt cggaatcgca gaccgatacc
     5041 aggatcttgc cattctatgg aactgcctcg gtgaattttc tccttcatta cagaaacggc
     5101 tttttcaaaa atatggtatt gataatcctg atatgaataa attgcagttt catttgatgc
     5161 tcgatgagtt tttctgatag ttagtcttta atgaatgcgg ttggcgcatc ggcgggcacc
     5221 ttgcgcgcgc tgtcgctgtt catgccgcgc agcatgtcga tggcatcgag cacacccttg
     5281 gcggcgggcg cagcccgcaa tttg
//
