LOCUS       NZ_CP060079             1934 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain G3/10 plasmid pSYM3, complete sequence.
ACCESSION   NZ_CP060079
VERSION     NZ_CP060079.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN15693146
            Assembly: GCF_014295275.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1934)
  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  JOURNAL   Unpublished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 1934)
  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_g310
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 181x
            Sequencing Technology             :: Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 05:39:25
            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)                     :: 5,044
            CDSs (total)                      :: 4,926
            Genes (coding)                    :: 4,666
            CDSs (with protein)               :: 4,666
            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)              :: 260
            CDSs (without protein)            :: 260
            Pseudo Genes (ambiguous residues) :: 0 of 260
            Pseudo Genes (frameshifted)       :: 80 of 260
            Pseudo Genes (incomplete)         :: 168 of 260
            Pseudo Genes (internal stop)      :: 50 of 260
            Pseudo Genes (multiple problems)  :: 37 of 260
            Pseudo Genes (short protein)      :: 3 of 260
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP060079.1.
            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..1934
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="G3/10"
                     /isolation_source="feces from healthy individual"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSYM3"
                     /geo_loc_name="Germany"
                     /collection_date="1954"
     gene            join(987..1934,1..39)
                     /locus_tag="H4P47_RS24835"
                     /old_locus_tag="H4P47_24835"
     CDS             join(987..1934,1..39)
                     /locus_tag="H4P47_RS24835"
                     /old_locus_tag="H4P47_24835"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001529700.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_016245711.1"
                     /translation="MQNPKLQNLTDYSPSDAPWDAHKSVSDDVGGIYLLAAEYERYGAR
                     MASCGGLLRFGWSTLKETGETRLRLREAHFCRVRHCPVCQWRRSLMWQARFYQSLPRIV
                     ADYPDARWMFLTLTVRNCAIGELGETLNRMNMAFQRLKDRKEFRPVQGWIRTTEVTRGS
                     DGSAHPHFHTLMMVPPSMFTRDYVKHDRWVELWRECLRVNYDPNVDVRAVKPRKPKDGE
                     SLASATAELVRGAVAETLKYSTKPADMVADPEWFLELTKQTHKRRFVATGGALKDILKL
                     DQETDADMVIGDDIPEGDDDGSRIAFEWKTESKKYRRSPSKDKAESD"
                     /name="protein rep"
     gene            698..1000
                     /locus_tag="H4P47_RS24840"
                     /old_locus_tag="H4P47_24840"
     CDS             698..1000
                     /locus_tag="H4P47_RS24840"
                     /old_locus_tag="H4P47_24840"
                     /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_023150476.1"
                     /translation="MAGSIRARSLYLYLRDNSGDKKWHQALRTKASGLICVVEGFGSIL
                     LGVVALKATPATTAIVRGCDHLQKFDSKRQPTGDTAMITRQMSHRPAWDGVHAKP"
                     /name="hypothetical protein"
     Typing          complement(1700..1888)
                     /name="ColpVC"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="88.947"
                     /coverage="98.0"
                     /evalue="1.39e-59"
ORIGIN
        1 cgtcgctcac cgtcaaaaga taaagctgaa tcagactgac agggtgtcgg ggcgcagccc
       61 tgaccacgac gtttttgaga ggacgccgct tgtcggcggt actccaaaaa cacatcttgt
      121 cctattggtt ctactccgat gcaggatagg gctaacgccg caaagtgacg tcactcaatt
      181 actgagttcg gtttccgaac tcagttggga caagatgtgt ttttggtaca ccgccatcac
      241 gatgtcggtg ccaaaaacga ttcgtcaggg ctgcgccccg acaccctgcc aacacctcac
      301 gcagtcagat taaaatctgc cagcgctcgc cgtttccgaa atcgtcaaac tctaaatcgt
      361 ggggtcccgc tggcttgcca gtgggttccg atttagtgat tgacgacatt gctgattgaa
      421 aaattggctg aggtggttgg attcacgaag tgaggccaac cacctggaag acggttttta
      481 attgtctggt accggataca accagaacga atggagttgg ttctgtcgtg atgcgaaaaa
      541 gtatgggttc gcaaatcaca gactaaatag atttacccaa ttccattcga gtgaggttgt
      601 tatgtttttt gaggttctta atcatgttga tagtgcgttg agcgttgctg tttcgctcct
      661 ggcgttgtgg cagtttttgg tggcgggtgg gcgttgaatg gctggttcga tccgcgcgcg
      721 atccttgtat ttatacttaa gggataactc tggcgataaa aaatggcatc aagccttgcg
      781 taccaaggct tcggggctta tttgcgttgt agaaggtttt ggaagtattc tgttgggagt
      841 ggtcgcctta aaagcgaccc ccgcaacgac ggccatcgtt cgggggtgtg accacctgca
      901 gaaattcgat tcgaagcgac aaccaacagg tgatacggca atgataacac gtcaaatgag
      961 ccatcgccca gcatgggacg gtgtgcatgc aaaaccctaa actccagaac ctcacggatt
     1021 actccccctc agacgcgccc tgggacgctc acaaaagcgt ttctgacgac gtaggtggga
     1081 tttaccttct cgcagccgaa tatgagcgct acggggcgcg tatggcttcc tgtggcggtt
     1141 tactgaggtt tggttggtct accctcaaag aaactggaga aactcgcctt aggctacgtg
     1201 aggcgcattt ctgccgtgtc cggcactgtc ctgtctgcca gtggaggcga tccctgatgt
     1261 ggcaagcccg tttttatcag tccctgccgc gtattgttgc ggattatcca gatgcacgct
     1321 ggatgttcct gaccctcaca gtgcgaaact gcgcgatcgg ggaattgggt gagacactta
     1381 accgaatgaa catggccttc cagcgactta aggatcgcaa agagtttcga cctgttcagg
     1441 gctggatccg caccacggaa gttacacgtg gaagtgacgg tagtgcgcac ccgcactttc
     1501 acactctgat gatggttcct ccctcaatgt tcacgcgaga ttacgttaaa catgaccgct
     1561 gggtagagct ttggcgagag tgtttgcgtg tgaattacga tccgaatgtt gatgttcgag
     1621 cagtaaaacc ccgcaagcct aaggacggag aatcattggc ttctgcaact gcggaacttg
     1681 tacggggcgc agtggctgaa accctgaaat attccacgaa gccggctgac atggttgctg
     1741 atcctgaatg gttcctcgaa ttgactaagc agacacataa gcgccgattt gtggctaccg
     1801 gtggcgcact caaagacata ctgaaactcg atcaggaaac tgatgccgat atggtaatcg
     1861 gggatgatat tcccgaaggc gatgatgatg gttcacgcat tgcttttgag tggaaaaccg
     1921 aatccaaaaa gtac
//
