LOCUS       NZ_CP104535             3396 bp    DNA     circular CON 06-OCT-2023
DEFINITION  Escherichia coli strain E10 plasmid p2, complete sequence.
ACCESSION   NZ_CP104535
VERSION     NZ_CP104535.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN30789313
            Assembly: GCF_025369715.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3396)
  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  JOURNAL   Unpublished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 3396)
  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                   :: 10/06/2023 03:59:01
            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)                     :: 5,188
            CDSs (total)                      :: 5,069
            Genes (coding)                    :: 4,839
            CDSs (with protein)               :: 4,839
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 230
            CDSs (without protein)            :: 230
            Pseudo Genes (ambiguous residues) :: 0 of 230
            Pseudo Genes (frameshifted)       :: 85 of 230
            Pseudo Genes (incomplete)         :: 148 of 230
            Pseudo Genes (internal stop)      :: 53 of 230
            Pseudo Genes (multiple problems)  :: 53 of 230
            Pseudo Genes (short protein)      :: 4 of 230
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP104535.1.
            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..3396
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="E10"
                     /isolation_source="Breeder"
                     /host="Poultry"
                     /db_xref="taxon:562"
                     /plasmid="p2"
                     /geo_loc_name="USA"
                     /collection_date="2017-06-13"
                     /collected_by="USDA"
     gene            complement(join(3137..3396,1..469))
                     /locus_tag="N5O77_RS25840"
                     /old_locus_tag="N5O77_25840"
     CDS             complement(join(3137..3396,1..469))
                     /locus_tag="N5O77_RS25840"
                     /old_locus_tag="N5O77_25840"
                     /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_157919132.1"
                     /translation="MALMVTRRYLLGGEYPSEEFVQASLEKYFFRQGFDIDTGSYIDLI
                     CRDKESRDVVWHIEVKGKTSQPGLDFRTCLGQLVQRMTKDNINYAIAVPRIKQYERLIE
                     ETSILAVSKLNLHWIFVGPDGSVTIKEPDSSTMKNGNGNGNGREVSLVNGGFKRFIPGD
                     FMPTCSYGKAPVVFKSSRREMWDWLDDFVISNGVIPSIADIKEEAESRGGKWTLSNVKI
                     EYQFWKIYHLYKGHFFYQSE"
                     /name="hypothetical protein"
     gene            complement(696..839)
                     /locus_tag="N5O77_RS25845"
                     /old_locus_tag="N5O77_25845"
     CDS             complement(696..839)
                     /locus_tag="N5O77_RS25845"
                     /old_locus_tag="N5O77_25845"
                     /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_261175630.1"
                     /translation="MATATNFDAWLDDVDGDYEEVMALYDSVQNVSDMGLYQCVEGGRG
                     DA"
                     /name="hypothetical protein"
     gene            complement(1052..1264)
                     /locus_tag="N5O77_RS25850"
                     /old_locus_tag="N5O77_25850"
     CDS             complement(1052..1264)
                     /locus_tag="N5O77_RS25850"
                     /old_locus_tag="N5O77_25850"
                     /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_089634954.1"
                     /translation="MSNIKPDSLIRITKRKNENGDETTDLEWKPGSKEAIATGAAAGAA
                     LGSAVPVIGTAVGAVIGGTLALIFG"
                     /name="hypothetical protein"
     gene            complement(2156..2347)
                     /locus_tag="N5O77_RS25855"
                     /old_locus_tag="N5O77_25855"
     CDS             complement(2156..2347)
                     /locus_tag="N5O77_RS25855"
                     /old_locus_tag="N5O77_25855"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /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_021314601.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNDLDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            2783..>2863
                     /locus_tag="N5O77_RS25860"
                     /old_locus_tag="N5O77_25860"
                     /pseudo=""
     CDS             2783..>2863
                     /locus_tag="N5O77_RS25860"
                     /old_locus_tag="N5O77_25860"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001333247.1"
                     /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="replication initiation protein"
                     /name="replication initiation protein"
     Typing          2505..2910
                     /name="rep_cluster_2370"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.892"
                     /coverage="93.0"
                     /evalue="3.81e-158"
ORIGIN
        1 taaaccctcc attcacaaga gaaacttctc ttccattacc attaccatta ccatttttca
       61 tcgtagagct atcaggttcc ttaattgtca cactgccatc aggcccaaca aatatccagt
      121 gtaaattcaa tttactaaca gcaagaatgc tcgtttcttc tattaatctt tcatactgtt
      181 ttattcttgg aacagcaata gcataattaa tattatcttt tgtcattctc tgcactaatt
      241 gtccaagaca agttcgaaaa tccaaccctg gctgtgatgt tttccctttt acttcaatat
      301 gccacacaac atccctagat tctttatcac gacaaataag gtcaatataa gatcccgtat
      361 ctatatcgaa cccttgtcga aaaaaatatt tttctaaaga agcttgaaca aattcctcgg
      421 aaggatattc accacctagt aagtaccttc tcgtcaccat aagagccaca acccctacgc
      481 atcctattta ctataacgtc atattttaag agttcctaca aagggaactc tctgtacgat
      541 tacgagtgat cattcgatat atttcgttga aatccatacc atgaatcaac atcttcgccg
      601 ccacatagcc tttctctaat caatttgagg aaagtatccc tagccacagc tgatgctaga
      661 aaaagagctt ctggatgatg attagagctc acgactcaag catcaccccg accaccctca
      721 acacactgat acaaccccat atcacttaca ttctgaacgg aatcataaag agccataacc
      781 tcctcataat cgccatcaac atcatctaac cacgcatcaa aattagtagc agtcgccatg
      841 ccaatcctcc attttttagt tttcaggagt taatttacat agtgataggg gctgttaagc
      901 aaataagttt ttaccttttt tgcctcatgc tctaaaagtg agcaagacag gcatttacca
      961 taacgcctca ttgctcgcat gagcgtaaaa aagcccgctt ttagcaggct accttccgcc
     1021 attcttgacg ggtgtttcgc tctaaacttg gttatccaaa aattaaagct aaagtcccac
     1081 cgatcacagc cccgactgca gttcctatta caggaacagc agaacctagt gctgctccag
     1141 cagccgcgcc tgtggcaatt gcctcttttg aaccaggctt ccattctaaa tctgttgttt
     1201 catcgccatt ttcattcttt ctttttgtaa tccggatcag actatcaggt ttaatattgc
     1261 tcattcgcac ctcacgtaag attgaaacgt atacaccaaa aacactctcc ctccacctag
     1321 gctacatttc aactacatat attaaaaacc ctgcatttac cataacgcct cattacgcgc
     1381 accgctcaga cggcctgagc gcgtttctga cgggaaaccg gtaaaacagg caacaaacca
     1441 cccgaaaacc cgccagaaac gcgcaggctc tgtttttacg gcatgcatga gtatgcgcac
     1501 aagtgcatag cgcggaaatt cacgccattc agccggggta agtcctgttt ccgatgttct
     1561 tcttacccga aaacggtgaa cggggacgca atttattgcg tggccgtgag gcgttgccgg
     1621 cacagccgga aaaaccattt tcagcacgtg caggaggccc aggaagaggg ggcggatgta
     1681 cgaatagctc agaggtcaga tctgacgtaa aaatgatgta aaagtgatgt acttttgatg
     1741 taattctgtt gtacacccgc gatctgacgt aaaagtgatg taattttgat gtacttttga
     1801 tgtaattctg ttgtacaccc gcgttctggg gtaaaagcag atgcaatttt gtagtttatg
     1861 tgtagtcgct gaacccatag ggtcatacga gcatgaccct ttcccggaaa aggacgcttt
     1921 ttagccagaa tcatccttaa cctgcggcgc cagcactcgg gagtggtcgt tttatatact
     1981 aaaaaatgac atacacctaa cgcagctgcg attttcatcg caacttcatg aaaaataaat
     2041 aaaaaataaa aaatacaggg attctgggta ttaccggggt aataatgtta agcgctaaca
     2101 caatgaaaat taaggcgatg ccggtattac cccggtaata cccagaacgg agccattacg
     2161 caccgtcctg ctgctcattc aggcgcgctg acaggcttcg gtaaaggcgt tccgcatcct
     2221 catggagttt ctcgcagaaa tcagcctcat gatccagatc caggtcatta agcctgtcca
     2281 gaagaagcag ggactgatcc tggatgaatt tagccatgtt aacggcagtc ttttgttgtt
     2341 tgttcatgaa agccccggcg cgaaagtgct tactgtacgt tctgatggtt ttccgcttcc
     2401 tcgctcattc gctcactccg ttcggtcatg agtctgcggc gagcggaggg aggataagca
     2461 gataacgtaa cggtaagcat aacgaaagct aaggacaagg gcgaaaaggc cacgccccgg
     2521 cggggcgttt ttccataggc tccgcccccc tgacaagcat cacagaatct gacgctcaaa
     2581 tcagtggtgg cgaaacccga caggactata aagataccag gcgtttcccc ctggtcgctc
     2641 cctcgtgcgc tctcctgttc cgaccctgcc gcttaccaga tacctgtccg cctttctccc
     2701 ttcgggaagc gtggcgcttt ctcatagctc acgctgttgg tatctcagtt cggtgtaggt
     2761 cgttcgctcc aagctgggct gtgtgcacga accccccgtt cagcccgacc gctgcgcctt
     2821 atccggtaac tatcgtcttg agtccaaccc ggtaagacac gactaatcgc cattgacaac
     2881 ggccactggt agacaggatg tgcgagagat gtatcgagag ttcttgaagt ggtggcctga
     2941 ctgcggctac actgaaagga cagatttggt gacatgtctc gcacaagact gttaccacgg
     3001 ttcagaagtt ccccaactta ctgaaccttc gaaaaaccac ctccccaggt ggttttttcg
     3061 ttttccgaga aagagattac gctttgagcg aatgaatctc aagaagatca tggcatttga
     3121 tgaacaaatg agtcagctac tcagattgat agaaaaaatg ccccttatac aagtgatata
     3181 ttttccaaaa ctgatactct attttaacat tagaaagcgt ccatttccca ccccgcgatt
     3241 cagcctcttc tttaatatca gcaatacttg ggatcacccc atttgaaata acaaaatcgt
     3301 ccaaccaatc ccacatttct cgccgagatg atttaaatac aacaggagct ttcccatatg
     3361 agcaagttgg cataaaatcc cccggaataa atcttt
//
