LOCUS       NZ_CP104507             4074 bp    DNA     circular CON 07-OCT-2023
DEFINITION  Escherichia coli strain E1 plasmid p4, complete sequence.
ACCESSION   NZ_CP104507
VERSION     NZ_CP104507.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30789304
            Assembly: GCF_025369875.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4074)
  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  JOURNAL   Unpublished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 4074)
  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 07:43:30
            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)                     :: 5,314
            CDSs (total)                      :: 5,202
            Genes (coding)                    :: 5,011
            CDSs (with protein)               :: 5,011
            Genes (RNA)                       :: 112
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 191
            CDSs (without protein)            :: 191
            Pseudo Genes (ambiguous residues) :: 0 of 191
            Pseudo Genes (frameshifted)       :: 78 of 191
            Pseudo Genes (incomplete)         :: 130 of 191
            Pseudo Genes (internal stop)      :: 35 of 191
            Pseudo Genes (multiple problems)  :: 44 of 191
            Pseudo Genes (short protein)      :: 3 of 191
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP104507.1.
            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..4074
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="E1"
                     /isolation_source="Broiler"
                     /host="Poultry"
                     /db_xref="taxon:562"
                     /plasmid="p4"
                     /geo_loc_name="USA"
                     /collection_date="2017-05-22"
                     /collected_by="USDA"
     gene            complement(join(3582..4074,1..1667))
                     /gene="mobQ"
                     /locus_tag="N5O81_RS26495"
                     /old_locus_tag="N5O81_26495"
     CDS             complement(join(3582..4074,1..1667))
                     /gene="mobQ"
                     /locus_tag="N5O81_RS26495"
                     /old_locus_tag="N5O81_26495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobQ family relaxase"
                     /protein_id="WP_052935848.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAIGPAGFSGKVRDWNDRTHAET
                     WRASWADHANRALANAGYEEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPVMPSLAARKVDFTQGRLPPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHTTERRHDRSWSQ"
                     /name="mobQ"
     gene            1846..2100
                     /gene="mobC"
                     /locus_tag="N5O81_RS26500"
                     /old_locus_tag="N5O81_26500"
     CDS             1846..2100
                     /gene="mobC"
                     /locus_tag="N5O81_RS26500"
                     /old_locus_tag="N5O81_26500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091746.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobC"
     gene            2632..3324
                     /locus_tag="N5O81_RS26505"
                     /old_locus_tag="N5O81_26505"
     CDS             2632..3324
                     /locus_tag="N5O81_RS26505"
                     /old_locus_tag="N5O81_26505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /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_052935847.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYEFLQQFRSTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIKPCVDELNKKSDLAVTVETIKKGRTVVALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(1310..1668)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1669..1845
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.438"
                     /coverage="100.0"
                     /evalue="2.610000000000001e-86"
     Typing          2633..3324
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.965"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(4..1754)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.801"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 actggctggc ggtcttctcc aagacagaaa gactccggcc atgtcttcgg ctggcggaga
       61 ttgcgggtat attgcggcca tgtctggcaa acctgcgtca gaagttgctc aaaggtcgca
      121 gaggaataaa cacgttgcag tggtggatgt tgaccgattt cgcttcggtc acagatataa
      181 ccactcctat cacgcattaa atcaacacgc tcaaagattc tggtgcggta tttctccagc
      241 tcgttccccc agagcgtata ttctccgttc cggttgtgaa gcagaaggta acaggtcatt
      301 tccccgttac caggcatggg ggcctcgcca taccccgtaa cgactgcgct cagtacccct
      361 gaatccataa cggcattgtc atttttcctg agctgttcag ctcgtcgctc cgcgcgacta
      421 cgttctgtat cctcctgctc cttccggcgc aattcctctt cacgtttaag caactggact
      481 ctgagagctg caaggccgga tgccccccac tgctgccact gtttttcaaa tgccgtctga
      541 ctcgcgggaa tgtcctgttt ctccaccttc cggtaatgct gtcgcaattt ttccatttgc
      601 tggctcagcg actggatttt tccctgttcg ctacggtatt ccggtgccgc ccattgcatc
      661 aggggaatac gggaaaaacc ggacgaaaac ggcgatgatt ttttcaggct ggcagcatga
      721 ctcatcgctt cctttcgttc ggtgttcagc tcttcccagc gtctgcgcgt cgcctgcata
      781 tctgccatca tcgacatggc attactggtg agtttccatg ccgcattact gtccttcggc
      841 aacgcttcga tgatgtcacg tagtgtgtac gaagttgcgt tgtcaggaag cacgatattc
      901 agaaggtcag ccacacggcg ggcaggctct gtcagcccgc tgttcctgag ttcagtgcgg
      961 gaaatctgta tttccaggtt aagcctgtta atcagacgat tctgttcgcc gcgttctgtt
     1021 tcgataccgc gtgtttccat cgcacaggca gactttccga ggtgaatacc aggcgttttc
     1081 tcaagcccct gtcgctcgta tgaacgatgg tctatctctt cctcataacc ggcgttcgcc
     1141 agtgctctgt ttgcatggtc agcccatgat gcacgccacg tctcggcatg tgtccggtcg
     1201 ttccagtccc tgacctttcc gctgaaccca gcaggtccga tagccctcgt ggtcagcatg
     1261 atgtgcgcat ggggatttgt tttatccatg tgatggaacg ccacatcagc aatcatgccc
     1321 tgactgacaa agttttctct gacaaaggcg agaacggttt cccgtgcggc atcctgcggc
     1381 agttcgtggg ggatggcgag ttcaatttcc cgcgcaagtt gtgagttctt ccggcgttcg
     1441 gccttctcaa cggcattcca gagttcggca cggttcgtac accaggcagg ggcggtggcg
     1501 ggggtcagaa tcacagcctc agccacaccg cttttgcggg tgtagtcgtg agtcagtccg
     1561 gtacgctcat caagcatcag tgaaccggaa cgataggcag cggaagctac ggcgctgtag
     1621 ccgctgcttc tggagataat tttcatgctg agatgataaa tcgccatttc tgccgtaatg
     1681 cctttttgta tttttctttc agccccgcag ggcgcacaca atcgaaacgg agtggagatt
     1741 gtataagtgc gcacttcgtg atttgccgtg cattatgcca gctcagtttt taaactacca
     1801 gtgacgcgct aaaatgcgat ttttcatcgc gcacggagtt acatcatgag cagaacgctc
     1861 gaacagaaga ttgctgatgc tgaggcgaga ttacagcgcc tgaaggcgaa gagccggagc
     1921 ctggacacag cgcagaaggt tgttgtgggt gctgcattgc tggcaaaggt cagaaagccg
     1981 gaggaggtgc agttgcgtgc ctggttactc cagttcctga aggcagaggt gacacgacag
     2041 gctgatgtga cgcgcatact gccgctgatt aacgagctgg aggcgctgcc agaacagtga
     2101 ttgtatcgtc cgctcaccgc agccccagcg accgagcgtt agcgagcgag tgggcgagga
     2161 agcggaagtg aatccgtcgc caggttgagc acatacgcac ggtttttcgg caggtgatat
     2221 gcgctgaacc cgcatgaata ctggatttcc acagggttgg agggggagta ttcggaactt
     2281 gcaattctgc tttcttgcaa catattgttt ttattggttt tttgttttca gtaccccaag
     2341 ttatccacag gctcgccgtt aagtttttag atcttgtttt taagatcttg tttttaatac
     2401 ttgttttagg agtgaaattc attaataaaa tcaatatgtt atagaggtat atgtggagga
     2461 atttaaggta tatgtggagg aatttaaggt gtttaggtgg aggaatttaa ggtaaaggtg
     2521 gaggaattta aggtgttatt cacagaaatg tgaggatata aaaaaaaata ttccacattt
     2581 cttatttgtg gggcacatta aagcatcacc acatttgaac gggatctttg tatgtcggac
     2641 ttgattgcct acaagtcgaa tgctttggtt gaggccagct acaagttgac cctacaggaa
     2701 caacgttttc tgttgctgtg tatcagtcga ttgaaatctg gtgctgatgc tgaattgcaa
     2761 aagacaatga ccattaccgc tgcggaatat tttgattcat tccctgacat ggggcggaaa
     2821 aatgccgagg ttcagttaca ggaagcgatc gatcgtttat gggacaggtc gatcattctc
     2881 aaggatgacg agaagcgtga ggagttccgc tggatccagt atcgggcaca gtatgctaaa
     2941 ggtgaggcca aggctcgaat aaccttttct gacgcggtaa tgccttatct gacgcaactg
     3001 aaggggcaat tcacgcgcgt tgttataaaa aacatatcag gtttatcaag tagttacagt
     3061 ataagaatat acgagtttct ccagcaattc cgcagtacgg gagagagaat tattgctctt
     3121 aatgactttc gttcaatgtt agggattgaa aataaataca aacaattcag agacttaaat
     3181 aaaatattaa taaaaccctg tgttgacgaa ctgaacaaaa aaagcgacct ggctgtaacg
     3241 gttgagacga tcaaaaaggg gcgcacggtt gtagccctgc attttcgctt caaggaagac
     3301 aaacagatca agatgacgat ctaaaatcga ttttaaggca cctaaaacat tccctgctgc
     3361 gttttttttg tgttagtagt gcgaaggtac tattgaagtg aaaaattgcg tcaaaaacgc
     3421 tctgatgcag cgaaaaaaga acccccaatt tttgggggcg gaaaaacaaa actatgcttg
     3481 cgttatgtga gtgtgcttct tgcattcatc cctgtcgatg agcatcgaag aacatcgacg
     3541 aacataacac gatgttaaac aaaacaaaat attgttcaca ttcactgtga ccaactgcga
     3601 tcatgtctcc tctcggtggt gtgtgttctt gcatcttcct cgcgccgcca ttcgtcccag
     3661 gtacgattga aacccagcga gcggaacaga tgatccggct gtttttctgg tgtgttgacg
     3721 gcagcaaaaa gcggtgcctc acgggttttc agatgaaact ccataagttc cggcgcaggt
     3781 gatatgtggc tgtctgcatc gtgatttacg gcaacaccat accctgcata ccgtaacccc
     3841 ttatcggtca gtgcactgat gaccagctgg ctgttatcgg ctgagggaac ggcaaacgcg
     3901 ggatacagcg taccattaag ccggacaaca ccgcccagag agtcatccac gcccatgacc
     3961 agtaaaagct gaagctggcg ggtttcccgg tcgacagaac tcattaccgg catcagcgtc
     4021 ggtggcagac gtccctgcgt aaaatccacc ttccttgctg ccagtgatgg catg
//
