LOCUS       NZ_CP060070             3214 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain G5 plasmid pSYM11, complete sequence.
ACCESSION   NZ_CP060070
VERSION     NZ_CP060070.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15693148
            Assembly: GCF_014295295.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3214)
  AUTHORS   Jenjaroenpun,P., Wongsurawat,T., Khan,N., Wassenaar,T.M.,
            Nookaew,I., Ussery,D.W. and Zimmerman,K.
  TITLE     Whole genome sequencing of five probiotic Escherichia coli strains
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3214)
  AUTHORS   Jenjaroenpun,P., Wongsurawat,T., Khan,N., Wassenaar,T.M.,
            Nookaew,I., Ussery,D.W. and Zimmerman,K.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-AUG-2020) Biomedical Informatics, University of
            Arkansas for Medical Sciences, 4301 W Markham St, Little Rock, AR
            72205, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: JAN-2020
            Assembly Method                   :: Unicycler v. 0.4.8
            Assembly Name                     :: UAMS_Ecol_g5
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 696x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 05:46:22
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,964
            CDSs (total)                      :: 4,845
            Genes (coding)                    :: 4,610
            CDSs (with protein)               :: 4,610
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 235
            CDSs (without protein)            :: 235
            Pseudo Genes (ambiguous residues) :: 0 of 235
            Pseudo Genes (frameshifted)       :: 88 of 235
            Pseudo Genes (incomplete)         :: 147 of 235
            Pseudo Genes (internal stop)      :: 43 of 235
            Pseudo Genes (multiple problems)  :: 42 of 235
            Pseudo Genes (short protein)      :: 4 of 235
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP060070.1.
            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..3214
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="G5"
                     /isolation_source="feces from healthy individual"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSYM11"
                     /geo_loc_name="Germany"
                     /collection_date="1954"
     gene            complement(1051..1263)
                     /locus_tag="H4P49_RS24490"
                     /old_locus_tag="H4P49_24485"
     CDS             complement(1051..1263)
                     /locus_tag="H4P49_RS24490"
                     /old_locus_tag="H4P49_24485"
                     /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_039509481.1"
                     /translation="MGDFERTYGAGADFDRIIDENNSEYFRDERQKAKNSKKEFSSFQD
                     ALVWAKANPGKTIVRSPDGVGFIEK"
                     /name="hypothetical protein"
     gene            complement(1373..1639)
                     /locus_tag="H4P49_RS24495"
                     /old_locus_tag="H4P49_24490"
     CDS             complement(1373..1639)
                     /locus_tag="H4P49_RS24495"
                     /old_locus_tag="H4P49_24490"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000262326.1"
                     /GO_function="GO:0008657 - DNA topoisomerase type II
                     (double strand cut, ATP-hydrolyzing) inhibitor activity
                     [Evidence IEA]; GO:0042803 - protein homodimerization
                     activity [Evidence IEA]"
                     /GO_process="GO:0030541 - plasmid partitioning [Evidence
                     IEA]; GO:0051290 - protein heterotetramerization [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II toxin-antitoxin system RelE/ParE family
                     toxin"
                     /protein_id="WP_000262326.1"
                     /translation="MVWTINYSDRALKSLRKMDKQNARRIVDFMDLRIAVAADPRQSGK
                     PLKGELGEFWRYRVGDYRILCEIRDDELVILAATIGHRREVYD"
                     /name="type II toxin-antitoxin system RelE/ParE family
                     toxin"
     gene            complement(1623..1847)
                     /locus_tag="H4P49_RS24500"
                     /old_locus_tag="H4P49_24495"
     CDS             complement(1623..1847)
                     /locus_tag="H4P49_RS24500"
                     /old_locus_tag="H4P49_24495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000879771.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF6290 family protein"
                     /protein_id="WP_000879771.1"
                     /translation="MLAIRLSDEIESRLDSLAKQTGRTKTFYAREAILAHLEDLEDYYL
                     SAETAARVRRGDEAVHSSEDVRKSLGLDD"
                     /name="DUF6290 family protein"
     gene            2393..2581
                     /locus_tag="H4P49_RS24505"
                     /old_locus_tag="H4P49_24500"
     CDS             2393..2581
                     /locus_tag="H4P49_RS24505"
                     /old_locus_tag="H4P49_24500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165998.1"
                     /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_000165998.1"
                     /translation="MTKQESAALNMAKFIRAQSLLLLEKLDVLDLDDEAADCERMHEQA
                     EALYQKLSARFGIQDGE"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2629..2856)
                     /locus_tag="H4P49_RS24510"
                     /old_locus_tag="H4P49_24505"
     CDS             complement(2629..2856)
                     /locus_tag="H4P49_RS24510"
                     /old_locus_tag="H4P49_24505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001046776.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_206659768.1"
                     /translation="MFGFSPGELMNLCPDERLLFVRMISAMLRRSGGDAGAVMFEAYRH
                     IVSDTNQARRSCMLDLLESVRHDYVHGGYT"
                     /name="hypothetical protein"
     Typing          116..605
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.13"
                     /coverage="81.0"
                     /evalue="0.0"
ORIGIN
        1 ggacgaacgc ggcggaatga tgtcggatga cgtcattttg cggcgtttgc cctatcctgc
       61 atcgtattaa aaaatgcagc tatggcgcgt acggtgccaa agataagccc ggagatattc
      121 cgcttcctcg ctcactgact cgctccgctc ggtcgttcgg ctgcggcgag cggtaccggc
      181 ttactggcgg ggcggaaatt tcctggcatc ttccaggaag aagcttaaca gggaagcaag
      241 aaggccacgg cgaagccgtt tttccatagg ctccgccccc ctgacaagca tcacgaaatc
      301 tgacgctcaa atcagtggtg gcgaaacccg acaggactta aagataccag gcgtttcccc
      361 ctggtggctc cctcgtgcgc tctcctgttc ctgcctttcg gtttaccggt gtcattccgc
      421 tgttatggcc gcgtttatct cattccacgc ctgacactca gttccgggta ggcagttcgc
      481 tccaagctgg actgtatgca cgaacccccc gttcagtccg actgctgcgc cttatccggt
      541 aactatcgtc ttgagtccaa cccggaaaga cacgacaaag cgccactggc agcagccact
      601 ggtaacaggt ttagaggagg agagtcttga aatttcgggt gcgataaggc tacactgaaa
      661 ggactatttt gtgactgtgc tcctccaagc cagttaccgc ggttcaaaag agcgtcaact
      721 cttgcgaacc ttcgaaaaag ccaccttgcc gggtggtttt ttcgtttaca gagctaagag
      781 attacgattc tccctaaatg atctcaagaa gatccgttta aaaaagcggg ttttatggtt
      841 ggatgaagtt cgtcttaccc agtcacatat tagatttatt tgaattacta ctaggtttcg
      901 taagccatgc aagaattcct gtaactaaca aaataggccc tgcaatgtac gtaacataga
      961 ctccaacata cgacactgtg aaacatatga gtacgtatat agccagtgtt gtccaaaaaa
     1021 tgactgccgt tttacagtga atccactctt tcatttttca ataaatccca caccgtctgg
     1081 agatcttact atcgttttac caggattagc tttcgcccaa accaaagcat cttgaaaaga
     1141 agagaattct tttttcgaat ttttagcttt ttggcgctca tctcgaaaat attcgctgtt
     1201 attctcatca attatccgat caaaatcagc accagctccg taggtacgct caaaatcccc
     1261 catttcctac ccccataaat ttaataaaaa aacagattta aaatatccaa cagacactct
     1321 tatttaccat aacatccgtt gtcagcatca aaaaaagccc gcatagcggg cttcagtcgt
     1381 aaacttcgcg gcgatggcca atggtggcgg caaggataac cagctcgtca tcccggatct
     1441 cacacagaat gcgataatct cccacccgat agcgccagaa ctcgcccagc tcacctttga
     1501 gcggcttccc tgactggcga ggatcggcag caactgcaat gcgtaaatcc ataaaatcca
     1561 caatccgtcg tgcgttctgt ttgtccatct tgcgtaacga tttgagcgcc cggtcggaat
     1621 agttaatcgt ccagaccaag tgacttcctc acgtcttcag acgaatgcac ggcttcatca
     1681 ccacggcgaa cgcgtgcggc agtttctgct gaaagataat aatcttccag gtcttccaga
     1741 tgcgccagta ttgcttcccg cgcatagaac gtctttgttc tgccggtttg cttcgccagc
     1801 gagtccagac gggactcaat ctcatcagat aaccggatag caagcatata aacctcctga
     1861 acaccatttg atatacatgt atagcaatag tatcgcaatc aacctaaaag aacaaaaaat
     1921 aatcttgctg gcccctcttg ataatccgta acgctgtcaa tatatccagc ttgagggctt
     1981 tcctcttaac tattgaaagg ataacgatta tgggtcttaa gccgggtccg aaacgaattg
     2041 ccgattcaac aggggaacct gataaacgcc agcgtgacaa taaaaaaacg ccggggaata
     2101 ctgacaaatt gaaacccagc aaatcctcaa aaaaataagt cagtagttaa aagccctccg
     2161 gggctttttt tgtacccgca gatcagtctg attgaacata acatctgttg cgtgcaccgc
     2221 ctgagaggct ctcagggcgt ttctacgacc tcacctgcaa aagaacacat cttaccccct
     2281 gaaaaccgct cagaaacgcg ctgatgattt ctgcgtacct gcatggctat gcactcaagt
     2341 gaatgaagta agatttcagt ctgcgatcac cataaaaccg ggaaaaagcc gtatgacaaa
     2401 acaggaatca gccgcactga acatggcaaa atttatccgg gcgcagtcgc tgctgctgct
     2461 cgaaaaactc gacgtgctcg atcttgatga cgaggcagcc gactgtgagc gaatgcacga
     2521 acaggcagaa gcgctttatc agaagctgag cgcacgcttc ggtatacagg acggcgaata
     2581 aagagacgaa aagaacgctc acttagacga aaagcgtatc cagggcaact atgtatatcc
     2641 accgtgtaca tagtcatgcc tgacgctttc gagcaggtcg agcatgcagg aacgacgagc
     2701 ttgattggta tcggacacaa tatggcgata cgcctcaaac ataacagcac ccgcatcacc
     2761 gcccgaacgg cgaagcatag cggaaatcat ccgcacaaag agcagacgtt catcggggca
     2821 aaggttcata agttctcctg gtgaaaaacc aaacatgaaa gcccccatct attaacgtca
     2881 gctgtgaacg cttcattaga agaaaatagg taaacccggg aaaaagatcc aaacgttaac
     2941 atcacaggta aacagaaacg tcgggtcgat cgggaaattc tttcccggac ggcgcggggt
     3001 tgggcaagcc gcaggcgcgt cagtgctttt agcgggtgtc ggggcgcagc cctgaaccag
     3061 tcacgtagcg ctagcggagt gtatactggc taaacttcag agatgccaag gaagggacag
     3121 gatatgtttt gtagcaccgc caccacggtg gcgatactcc aaaacgcctg gtcagggcac
     3181 agccccgaca ccccagagcc gactgtaggt cact
//
