LOCUS       NZ_CP080131             3553 bp    DNA     circular CON 17-FEB-2024
DEFINITION  Escherichia coli strain PK8568 plasmid pPK8568-3kb, complete
            sequence.
ACCESSION   NZ_CP080131
VERSION     NZ_CP080131.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN20348874
            Assembly: GCF_019428645.1
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 08:09:26
            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)                     :: 5,043
            CDSs (total)                      :: 4,925
            Genes (coding)                    :: 4,682
            CDSs (with protein)               :: 4,682
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 243
            CDSs (without protein)            :: 243
            Pseudo Genes (ambiguous residues) :: 0 of 243
            Pseudo Genes (frameshifted)       :: 87 of 243
            Pseudo Genes (incomplete)         :: 151 of 243
            Pseudo Genes (internal stop)      :: 37 of 243
            Pseudo Genes (multiple problems)  :: 34 of 243
            Pseudo Genes (short protein)      :: 3 of 243
            CRISPR Arrays                     :: 4
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP080131.1.
            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="PK8568"
                     /isolation_source="chicken"
                     /db_xref="taxon:562"
                     /plasmid="pPK8568-3kb"
                     /geo_loc_name="Pakistan: Faisalabad"
                     /lat_lon="31.41 N 73.11 E"
                     /collection_date="2021-04-11"
                     /collected_by="Mashkoor Mohsin"
     gene            join(3426..3553,1..196)
                     /gene="mobA"
                     /locus_tag="KZY03_RS24950"
                     /old_locus_tag="KZY03_24950"
     CDS             join(3426..3553,1..196)
                     /gene="mobA"
                     /locus_tag="KZY03_RS24950"
                     /old_locus_tag="KZY03_24950"
                     /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            complement(483..1097)
                     /locus_tag="KZY03_RS24955"
                     /old_locus_tag="KZY03_24955"
     CDS             complement(483..1097)
                     /locus_tag="KZY03_RS24955"
                     /old_locus_tag="KZY03_24955"
                     /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            1417..2142
                     /locus_tag="KZY03_RS24960"
                     /old_locus_tag="KZY03_24960"
     CDS             1417..2142
                     /locus_tag="KZY03_RS24960"
                     /old_locus_tag="KZY03_24960"
                     /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            complement(2347..2460)
                     /locus_tag="KZY03_RS25460"
     CDS             complement(2347..2460)
                     /locus_tag="KZY03_RS25460"
                     /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"
     gene            complement(2948..3142)
                     /locus_tag="KZY03_RS24965"
                     /old_locus_tag="KZY03_24965"
     CDS             complement(2948..3142)
                     /locus_tag="KZY03_RS24965"
                     /old_locus_tag="KZY03_24965"
                     /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"
     Typing          3178..3417
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="7.6e-123"
     Typing          complement(2389..2913)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.274"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          3..193
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.438"
                     /coverage="99.0"
                     /evalue="5.130000000000001e-32"
     Typing          3427..3551
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="4.18e-19"
ORIGIN
        1 acgggcggca gctctcggta agaaagttaa ttcactgact gatgaccgag tgctgaaaga
       61 agtcatgcga ctgggggcgt tgcagaaaaa actctttatc gacggcaagc gtgtcgggga
      121 cagagagtat gcggaggtgc tgatagctat tacggagtat caccgggccc tgttatccag
      181 gcttatggca gattagcttc ccggagggaa actgtcgaaa acagacggta tgaacgccgt
      241 aagtccccaa accgatcgcc attcactttc atgcatagct atgcagtgag ctgaaagcaa
      301 tcctgacgca tttttccggt ttaccccggg gaaaacatct ctttttgcgg tgtttgcggc
      361 agaatcgcgt tcagcgcgtt ttagcggtgc gcgtaatgag acgttatggt aaatgggagc
      421 gttagaaaca gtcccattta cttgagtggg ggcagttggc catataaaaa atggtcaact
      481 gtttaaaata gatctttttc agaagctcgg cattctttgc aatatgaatt tattatttcc
      541 ccagccattg tttttcgcac gccaaaaaat ttaacaattt cttcgtggct ggttgcttta
      601 gttttcaaac attttgggca aatgcgtggt aattttatgt tgggtgtaat tccggttttc
      661 tttctttctt tctttttgtt gctgttgcta attgttatgc ctttagcttt tttgtttaaa
      721 tattctttta gaggagttga gtcgaatata ttagcgccat tggttagagg gtcattcctt
      781 gttgattggt atctagttaa tatccccaat gcctctaggt tactaacccc gcgttgaatt
      841 gttcttttag atacacctat tcttgatgca atggtaccaa ttgacggaaa agatattgac
      901 tcccctgact caggccattg atgcatcaat atattcagca gaatacacat ctcagtactc
      961 ccaataccaa gatcaccttg cagcataagg aggctatttg gtatagccgt ccacccatgt
     1021 atggttgcat catctcccca gtgagtagtg attaatgact cttttttttg ttctttctgt
     1081 gcgttttttg tgctcataga tgcttttctc gcgaaaaaaa aatcaaatgt gaacagttac
     1141 tacctaacta ctcttaatat aagagtagtt aggtagtaac atgtatcttt taggatgaca
     1201 taaatgtcat ccatttgctc tttttttata tagaacttaa gttgagtcca ctacctaaga
     1261 gttatgctct tagtggctat ccaagtcgag gcttggaagc gcattgtaca aaattcttcc
     1321 tgtattggat gcgtccatac agtggtctgt taactgcggt taagagacgc aaaaaggcct
     1381 gcatatgcag gcctttttgc tatctagagg tcaaaaatgg caagtatgga aacagagcag
     1441 caaccacaac aaactactga gcaaatcgaa gtaaaaacaa agcgagtgca gtgctttatt
     1501 gatgggtata atttatatca tgcaattgaa gagactggta ataaagctct tcattgggtt
     1561 gatcttaaat ctttatgcaa gagatacctt cctaaaaatg catctattga taatgttttt
     1621 tggttttccg ctaagccatc acatttatca agagccataa atgaaaatta tcaaaattac
     1681 accaacgctt taaccgaatg tggtgttgat gttatcggtg ggcgttttaa aaaaaagaat
     1741 gtaacgtgcg aagctgataa tggatgtggt ggagttttcc ataagcatga agaaaaagag
     1801 tccgatgtta atttggctat aagtctagtg tctggtgcgt gtaatgatga gtatgatata
     1861 gccattatta tcactgcgga ttctgactta tgccccccta ttaaatacgt aagagagcga
     1921 ttccctaata aagagctttg gcttgtagct cctccgggga gaatcaggcg agcgacagat
     1981 ctctgctctc tgtcatcgag aagtatggag atcaagaatg atgctttgag agcctgctgt
     2041 atgcgtgatg agttctacaa agatggagta cttgtagcca gaaggcctca ggaatggcga
     2101 gctgttgcca ataccaggca aagaagggct agaagtcgtt aggctttgtt gacgcagcta
     2161 gcgcaaggag attaatctaa ctaggttgaa aacgaaaaaa ccgccttggc gggcggtttt
     2221 tcgaaggttc atagagttgg cgctctttga accgaggtaa ctggctttga ggagcacagt
     2281 cgccaaaact tgttctttca gtttagcctt atcaggtgca taacttcaag actcaactcc
     2341 tctaaatcag ttaccaatgg ctgctgccag tggcgttaag tcgtgtcttt ccgggttgga
     2401 ctcaagacga tagttaccgg ataaggcgca gcggtcgggc tgaacggggg gttcgtgcac
     2461 acagcccagc ttggagcgaa cgacctacac cgaactgaga taccaacagc gtgagctatg
     2521 agaaagcgcc acgcttcccg aagggagaaa ggcggacagg tatccggtaa gcggcagggt
     2581 cggaacagga gagcgcacga gggagcttcc agggggaaac gcctggtatc tttatagtcc
     2641 tgtcgggttt cgccacctct gacttgagcg tcgatttttg tgatgctcgt caggggggcg
     2701 gagcctatgg aaaaacggca tcggcgctgg cttgttccgg tgctttgctt tttgctcaca
     2761 tgttctttcc ggcgttatcc cctgattctg tggataaccg tattaccgcc tttgagtgag
     2821 ctgacaccgc tcgccgcagt cgaacgaccg agcgtagcga gtcagtgagc gaggaagcgg
     2881 aagagcgtct gacgtggcat tttctcctta cgctccgcta tgccgttctg catcctgtcc
     2941 gggtgcgtta tatcccggtg cgattttccg cttcaaagcg tgtctgtatg ctgttctgaa
     3001 gttcttccgc gagttcgtgc agcttctcac acatggcggc ctgttcgtca gcatcaagtg
     3061 cgtccagttt ttcgagcagc gtcaggctct ggctttttat gaatcccgcc atgttgagta
     3121 cggtttgctg ctgcttgttc atctttctgt tttctccgtt ctttctgtca tctgcgttgt
     3181 gtgattatat cgagtaccac ttttcgactg ttttaccgcc ggtattctgc tgtctgactc
     3241 tttgacgggc atttctgtca gacaacactg tcactgccaa aaaactgccg tgcttttgtc
     3301 ggtaattcga gcttgctgac aggacaggat gtgcaattgt tataccgcgc atacatgcac
     3361 gctattacaa ttaccctggt cagggctttg ccccgacacc catgtcagat acggagccat
     3421 gttttatgac aaaacgaagt ggaagtaata cgcgcaggcg ggctatcagt cgccctgttc
     3481 gtctgacggc agaagaagac caggaaatca gaaaaagggc tgctgaatgc ggcaagaccg
     3541 tttctggttt ttt
//
