LOCUS       NZ_CP104544             5463 bp    DNA     circular CON 07-OCT-2023
DEFINITION  Escherichia coli strain E6 plasmid p5, complete sequence.
ACCESSION   NZ_CP104544
VERSION     NZ_CP104544.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30789309
            Assembly: GCF_025369915.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5463)
  AUTHORS   Feng,A., Leigh,S.A., Akter,S., Wang,H., Pharr,T.G., Evans,J.,
            Branton,S.L., Landinez,M.P., Pace,L. and Wan,X.-F.
  TITLE     Genomic Diversity, Pathogenicity and Antimicrobial Resistance of
            Escherichia coli Isolated from Poultry in the Southern United States
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5463)
  AUTHORS   Leigh,S.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (10-SEP-2022) Bond Life Science Center, University of
            Missouri, University of Missouri, Columbia, MO 65201-8522, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.9b
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100%x
            Sequencing Technology             :: Oxford Nanopore; Illumina MiSeq
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 10/07/2023 07:35:50
            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)                     :: 5,147
            CDSs (total)                      :: 5,028
            Genes (coding)                    :: 4,836
            CDSs (with protein)               :: 4,836
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 87
            ncRNAs                            :: 10
            Pseudo Genes (total)              :: 192
            CDSs (without protein)            :: 192
            Pseudo Genes (ambiguous residues) :: 0 of 192
            Pseudo Genes (frameshifted)       :: 82 of 192
            Pseudo Genes (incomplete)         :: 113 of 192
            Pseudo Genes (internal stop)      :: 37 of 192
            Pseudo Genes (multiple problems)  :: 39 of 192
            Pseudo Genes (short protein)      :: 2 of 192
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP104544.1.
            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..5463
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="E6"
                     /isolation_source="Broiler"
                     /host="Poultry"
                     /db_xref="taxon:562"
                     /plasmid="p5"
                     /geo_loc_name="USA"
                     /collection_date="2017-06-02"
                     /collected_by="USDA"
     gene            61..987
                     /locus_tag="N5O76_RS25570"
                     /old_locus_tag="N5O76_25570"
     CDS             61..987
                     /locus_tag="N5O76_RS25570"
                     /old_locus_tag="N5O76_25570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /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_001736644.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIEGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     PTQQKEQLRELRKRWEVKHNEHMRKNGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIMEWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQDRTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            990..1523
                     /locus_tag="N5O76_RS25575"
                     /old_locus_tag="N5O76_25575"
     CDS             990..1523
                     /locus_tag="N5O76_RS25575"
                     /old_locus_tag="N5O76_25575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000168774.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQNLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTMLDRNYNATAAVYQKVVILED
                     KLAEKPVTGKNRKN"
                     /name="hypothetical protein"
     gene            1744..2868
                     /locus_tag="N5O76_RS25580"
                     /old_locus_tag="N5O76_25580"
     CDS             1744..2868
                     /locus_tag="N5O76_RS25580"
                     /old_locus_tag="N5O76_25580"
                     /inference="COORDINATES: protein motif:HMM:NF013211.3"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_function="GO:0140911 - pore-forming activity [Evidence
                     IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA];
                     GO:0050829 - defense response to Gram-negative bacterium
                     [Evidence IEA]; GO:0031640 - killing of cells of another
                     organism [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin-like pore-forming protein"
                     /protein_id="WP_021529456.1"
                     /translation="MSGGDGRGPGNTGLGHNGGKPSGNVNGSSGHGGPSSGGGYHYNPG
                     KGPASTVGPDGEVHINITGGMEKDPPGKHHGNGGSGNGHGAGNHNSNSGGNGKTTSIPG
                     WSPDSGKPGRYLPTNKDKLIKGLIQSIDDHSGTYTIHYTGGAVATVTVPNGDVNKMNVH
                     YNIGSGPSSGNKLTRDTIKSFLEFKAENEANAVNDAISKVNDFYKELASKYGDKLEKEA
                     KALADEAKGKKIRNANEAIKAFDRYKDVLNKKFSVSDREAIAKALESLNKDQMAKQLKI
                     FGKAFGVVGEAIQWGGFISGLVKGFRTGDWNEAFISGEKIAVGKVASVMVTVAFSAMAV
                     NPIGILGFAVIMAVTSALITDERLKQLNSFINGI"
                     /name="colicin-like pore-forming protein"
     gene            3669..4688
                     /locus_tag="N5O76_RS25585"
                     /old_locus_tag="N5O76_25585"
     CDS             3669..4688
                     /locus_tag="N5O76_RS25585"
                     /old_locus_tag="N5O76_25585"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221104.1"
                     /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_001271364.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREDAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKANSSENQSDKGKKS
                     AAVRWTANDDKRRRALDMYILGASTEDIAVAVGVSSRTIRRWMDNSGEWLTKKQIIKC"
                     /name="replication initiation protein"
     gene            complement(4949..5347)
                     /locus_tag="N5O76_RS25590"
                     /old_locus_tag="N5O76_25590"
     CDS             complement(4949..5347)
                     /locus_tag="N5O76_RS25590"
                     /old_locus_tag="N5O76_25590"
                     /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_001222916.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKEIKYDLETSPNPDA"
                     /name="hypothetical protein"
     Typing          3670..4444
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.907"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          62..984
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gcacttatat gtttctctcc ttcgtcgaga aacagtgcgc tcctgcggag ggctgaaacc
       61 gtggcgacct atcacctcag cgttaagttt ggtggcaagg gacaggctgc aaaccatgcc
      121 gattacatcg agcgcaaaga gaaataccgc gaccgtcaag atttggaata ttccgcacac
      181 ggaaacatgc cggaatgggc gcgagataat ccctcccatt tctggcaggc ggctgaccag
      241 tttgaacgtg caaacggttc gacttatcgg gaactggaga tagcgctgcc ccgtgaactg
      301 acaccggaac agcgccttga actggtgcag gattttgtac gtcaggaagc tggcgaacgg
      361 catgcatgga gttttgccat tcacaatccg aaagcgagca ttgagggagg cgaacagcct
      421 catgcgcata tcatgatgag tcagcgtgtg aatgatggca ttgaacgtac accggaacag
      481 tatttccggc gctataacgc caggtatccc gagcggggag gtgcgaaaaa ggattcagga
      541 agcctgactc ccactcagca aaaagagcag ttgcgggaat tgcgaaaacg ctgggaggtg
      601 aagcacaacg aacatatgag aaaaaatggc tttgaaaggg gcttcattga ctgtcggacg
      661 ctgaaagaac agggcattga acgacgtccc gaagtgcatc tgggttttga agctgccgga
      721 cggcttgatg atgcccagcg tcatgacatc atgcaaaaac ggtctgaacc ggactattcc
      781 cgccatcttg aacaggcgcg aacggtcggg catgacatca tggaatggct ggacactccg
      841 gttaagcaac atgaactggt cagaaggctg caacatgatg ttgcgcggga gcatggcttt
      901 gacatgagag acagagtgag cagacaggac cgaactgaac ctgaacgggt taaatcaccg
      961 tcacgtggat tttctatggg attctgaaca tggccagcac agaagaaaaa ttactcacgc
     1021 tcctgttatc ggtggagcat ttgcaacata ccgcaatgga gcaacagaaa gctgttgctg
     1081 attctctggc tgtggcaagg gaaacacttc gcggatatcg ggatatttct gacggtgtgg
     1141 caaaacaggt cagggatgaa gtcagaaatg aggtgcagaa tctggacgta gcagggctga
     1201 taggtgagcg catcagccag gattttcagc ggctggaaga gtcagtcgca aacatgaagg
     1261 caaacgcgga tgccctgaac agggatattg cgacaattca cagcaatatc gtgcaggaat
     1321 acaacaccct taaagggtat agctggaaat ggctgggtgg ggtgtcagtg gcttttctag
     1381 ttatgttctg tgtgctcgga tggggaatga aaacaatgct cgacaggaac tacaacgcca
     1441 cagcggcggt gtatcagaaa gttgtgatac tggaagataa actggcggaa aaacctgtca
     1501 cgggtaagaa ccggaaaaac tgacgcgctt cgcttgtcca acgcctcacg gacagcgaaa
     1561 ggatttcgcg ttccgttcac cgttttcatg agtgattcct ccgaactgcc aaaaaatatc
     1621 cctccctgac ttgacagaaa aaataatggc gagtactttt tgatctgtac ataaaaccag
     1681 tggttttatg tacagtatta actatgtaat taattgtttt aacgattaaa agagggaatt
     1741 tttatgagtg gtggagatgg tcgtggccct ggtaatacag ggcttggaca taacggtggt
     1801 aaacccagtg gaaacgtgaa tggctcatct ggacatggag gaccatcatc tggcggtggg
     1861 tatcattaca atccgggaaa aggtcctgca agcactgtag gtcctgacgg ggaggtgcat
     1921 atcaacatta ccggtggtat ggaaaaagat cctccaggaa aacatcacgg taatggtggc
     1981 tcaggtaatg gtcacggtgc tggaaatcat aacagcaatt caggcggcaa tggaaaaaca
     2041 acgtctattc ctggatggag ccctgactct gggaaacctg gcagatattt accgacaaat
     2101 aaagataagt taattaaggg acttattcag tcaatagatg accattctgg aacgtacact
     2161 atccattata ctggtggtgc agtagctaca gtaactgtac caaacggtga tgtgaataaa
     2221 atgaatgttc actataatat cggtagtggg ccgtcatcag gtaataaact gactcgtgat
     2281 actataaaaa gctttttaga attcaaggca gaaaatgaag ctaatgctgt aaatgatgca
     2341 ataagcaaag ttaatgactt ttataaagag ttagcatcaa aatacggcga taagttggag
     2401 aaagaagcca aggcactagc cgatgaagct aaagggaaaa aaattcgcaa tgctaatgag
     2461 gcgattaaag cctttgatag gtacaaggat gtgcttaata agaaattcag cgtatccgac
     2521 cgagaagcga ttgcaaaagc actggagtct cttaataaag atcaaatggc taaacagtta
     2581 aaaatttttg gtaaggcctt tggtgtcgta ggtgaggcta ttcagtgggg gggatttatc
     2641 agtggcttag ttaaaggatt cagaactggt gactggaatg aggcttttat aagcggggaa
     2701 aaaatcgcag tcggcaaggt agcatctgtt atggttacag tggcatttag tgctatggca
     2761 gtaaatccta ttggtatttt agggtttgca gtaattatgg cagtgactag tgccttaatt
     2821 acagatgaaa ggctgaaaca actaaacagc tttattaacg gcatttaata aacaaaaggt
     2881 cgtaccgttt gatatggtat gacctttatt ttgtttttct atcgcttttt gttggttata
     2941 aagtaataga ctgtaaaaat caatccaaat ggaggtagtg ataatataat gcatattata
     3001 aaaccccagt taacgaagtt aaaagttgtt tttgttagta agggtgcttg cttatttatt
     3061 agtaatagac aaaaagggta tgtggacgat ccaaaaagag atataagtat aaatataaat
     3121 aattctatac ttgttgggct tagattcaaa cttgcgatga taaaagataa aatgtaaaag
     3181 gataaggcaa ggataaaatt ccttaaatag aattccatat ctattttttt catttataaa
     3241 atcctcgtta gttaaatgtt tataatattg ccttacttta tccataaatc tagaagtagt
     3301 tatcacaaaa gttacttttt tgactcgttc gcccttttga acggtcgaaa ctgtttgcga
     3361 atcgctttcg tgcatagtta tgcaacgccc tgaaagtgat tctgacgcat ttttctggtt
     3421 tggcctggtg tttccttgtc tttttgcgtt ttttgcgcca gaaagcgact gagggcgttt
     3481 taaggggtac gtacaacggg agttatggta aatggatcgg ttttgcggga aggctcgaca
     3541 ggttttgttg ttgggggtag tgtaagcgac tgaaaaacaa acgcccctga aattcgtgtc
     3601 tctccgccaa gattgtcacg agaatacagg ggcgaggtcg gtcgataacc tggaaggaat
     3661 cgtaacacat gagcgccgcg cttcaatact tcgaagaaaa tttaccccac cgcccctatc
     3721 acacggatga tctcgctttc ggccttcgca tctccggcaa agggcgtgcg cttcttgcgc
     3781 ggtacatcca gcagaaccag cctcatgcgc agttctggct ggtttttgac gttgaccgcg
     3841 agggggctgc gattgactgg agcgaccgga acgcccccgc gccgaacatc accgttaaaa
     3901 atcctgtgaa cggacacgct cacctgctct acgcactcaa catcgccgtg agaaccgcgc
     3961 ctgatgcctc ggttaaggcg ctgaaatatg ccgcagcggt tgaacgttcg ctgtgtgaga
     4021 aactttgtgc tgatgtgaac tacagcggcc tgatttgcaa aaatccgttc cacctggaat
     4081 ggcaggtgat ggagtggcgc gaggacgcct ataccctcga tgaactggca gattatctcg
     4141 atttgagcgc ctcagagcgt cgtagcatcg ataaacatta cgggatgggg cgaaactgcc
     4201 acctgttcga aatgacgcgc aaatgggctt acagggcgat tcgtcagggc tggccagcgt
     4261 tctcacagtg gcttgaagcg gtgatccagc gtgtcgaaat gtacaatgca tcgcttcccg
     4321 ttccgctttc actggctgaa tgtcgggcta ttggcaagag cattgcgaaa tacacgcaca
     4381 ggaacttcac gccggaaact ttcgcacagt atgtggctga tacgcacacg ccagaaattc
     4441 aggcagcacg cggtcgcaag ggcgggaagg ccaattcgtc agaaaatcag tcggacaaag
     4501 ggaaaaaaag cgccgctgtt cggtggactg ctaacgacga caaacgtcgt agggcgcttg
     4561 atatgtatat cttgggagcg tcaacggaag atattgcagt ggcggttggt gttagcagcc
     4621 ggactattcg acgctggatg gataattctg gagaatggct aaccaagaaa caaataatta
     4681 aatgttagtt aacaaagaag caacactacc ccccgttttt tgttaatggg atgttaaatt
     4741 cgcggacatg aacaagccta tatcagataa cagcgccttt cggcgtcttt ttgagcagcg
     4801 ggctttccgg cggttttctc ctctcagccc agcaatggtg cggcttaccg catgattgag
     4861 gtggtcgtgc tcgccgcagt ctcatgaccg agcgtagcga gcgaatgagc gaggaagcac
     4921 cagggaaccg gaacacggat ggaggcactt acgcgtctgg gtttggggat gtctccagat
     4981 cgtacttaat ttccttaagt gcctgtaata tcctgtcttt tttatagcat agctcgcctg
     5041 tttttgtgtc taccagtcct gcttcgatca gtagcccagc cgcgagaaag agtcggtgat
     5101 tgcgttctcg tcgttgtttt tttccctcga ttcgtttttg gaccgcctgt tttcgttcgc
     5161 tctcctgtgc ctgtaagtcg tttttttccg ctgttgccag tacgtggagg agtttgcgtt
     5221 cctgttctgt gagtcctgct tcgttgtcga gcaggtcaat aatctgtctc tgtcgtgcgg
     5281 tctgttctcc gagcttcctg atgaatccga tccgtttctt cagccattcg atgttgctga
     5341 tgcgcatgtt cgtggtgctc cctggtgttt ttttgcggtg tgttgtggtc gtgcagtata
     5401 tcgcttgcgg tcggcgggtg cagggggtat cttccgtgct aattcgtaaa attagaagga
     5461 agc
//
