LOCUS       NZ_CP060071             2350 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain G5 plasmid pSYM8, complete sequence.
ACCESSION   NZ_CP060071
VERSION     NZ_CP060071.1
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 2350)
  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  JOURNAL   Unpublished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 2350)
  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
            CP060071.1.
            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..2350
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="G5"
                     /isolation_source="feces from healthy individual"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSYM8"
                     /geo_loc_name="Germany"
                     /collection_date="1954"
     gene            complement(join(2114..2350,1..492))
                     /locus_tag="H4P49_RS24515"
                     /old_locus_tag="H4P49_24510"
     CDS             complement(join(2114..2350,1..492))
                     /locus_tag="H4P49_RS24515"
                     /old_locus_tag="H4P49_24510"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /GO_process="GO:0015074 - DNA integration [Evidence IEA];
                     GO:0006310 - DNA recombination [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="site-specific integrase"
                     /protein_id="WP_012564910.1"
                     /translation="MGNSKRNIKKLNDNFREDILDYAIAHNLKCANALAILYATGCRPD
                     ELQTGVTVNYDSKKNEIEFRIIGSKLNRRMRRGIGVRKIKVKINNENARFFKNIVDKFI
                     ENPMSYDHKIKIESAKAFSGYITKISKKLWPRKTYHASAYSFRHAKATELKNSDYDKIE
                     IAQIMGHASVRSQQSYGRKSKKSKGGFDDIADVETNVKPRGGDRLLRFKIANKNKAAAK
                     IADTSTPSSPPPAPVRRFKM"
                     /name="site-specific integrase"
     gene            complement(861..1607)
                     /locus_tag="H4P49_RS24520"
                     /old_locus_tag="H4P49_24515"
     CDS             complement(861..1607)
                     /locus_tag="H4P49_RS24520"
                     /old_locus_tag="H4P49_24515"
                     /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="helix-turn-helix domain-containing protein"
                     /protein_id="WP_172687180.1"
                     /translation="MDIGNILNESLNVEYSKLDLFLEKYDLTPEQKVEVYEFHAKASKK
                     NKTLVISETKENKFKSISEGVEYVHLFPKNLKLLIKKYGLNTNELLVLTEIMESMLSHG
                     NLLINFSQKTLCELTEINKSTMSKTFKSLKQKQCLIEKNGHIYLNSVIFMKGLPHKLFI
                     QFRDHFLNSISYKLDDEEEFEKVFDDNFIKAYEKNLKEIKKKKQQIKEKKISKALDNFE
                     KEISEEWKEKFKDEEENFEFGFESEM"
                     /name="helix-turn-helix domain-containing protein"
     Typing          complement(1870..2053)
                     /name="Col(IRGK)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.459"
                     /coverage="100.0"
                     /evalue="1.26e-89"
ORIGIN
        1 tatttcgatt ttatcataat cggaattttt caattccgtt gcttttgcat gtctgaaaga
       61 atatgcagaa gcatgatagg ttttcctggg ccatagcttt ttcgatattt ttgttatgta
      121 cccggaaaat gctttggcac tttcaatttt gattttgtga tcatatgaca ttgggttttc
      181 aataaattta tcaacaatgt ttttaaaaaa tctggcattt tcattattga tttttacttt
      241 tatttttcta acccctatgc ctcttctcat tcttctattt agttttgatc caattattct
      301 aaattcaatt tcattttttt tgctgtcata gtttacagta actccggttt ggagttcgtc
      361 cggacggcaa cccgttgcgt ataaaatagc aagtgcgtta gcacatttta gattgtgcgc
      421 gatcgcataa tctaaaatat cctctctaaa attatcattt agttttttta tatttctttt
      481 tgaattaccc atattgattt ttcctcattg caaattaaaa gaaccggaaa tttcaaaaat
      541 tcgctttgct caaatttgaa ataccgtaaa acccaaaccc tcccccctta tgttcaattt
      601 ttcgctatcg ctcaaatcga acaacgaccc ccggttgggg gtggcaattt tatggccttc
      661 gctttgctct atccctaaaa tgccttgttg ttccacccaa aaagacgggt tgaaacaact
      721 acttatagta ctgttataac cgggtggaaa atgctgtcaa tatttgaaat gtggagaatc
      781 aatggataaa aaaaatccct tagtggaata gaatttattt ctatttcagt aagggattcg
      841 cctgcccggc gagggcggtt ttacatttca gattcaaaac caaattcgaa attttcctct
      901 tcgtctttaa acttttcttt ccattcttca gaaatttctt tttcaaaatt atctaatgct
      961 tttgatattt tcttttcttt tatctgttgt tttttctttt taatttcttt gagatttttt
     1021 tcatatgctt taataaaatt atcgtcgaag actttttcaa actcttcttc atcatctaat
     1081 ttataagaaa ttgaatttaa aaaatgatct ctaaattgaa taaacaattt atgcggcaaa
     1141 cctttcataa atattacaga atttaaataa atatgcccgt ttttctcaat taaacactgc
     1201 ttttgtttaa ggcttttaaa tgtttttgac attgtagatt tattaatttc tgttaattca
     1261 caaagagttt tctgtgaaaa attaattaat aaatttccgt gtgaaagcat cgattccatt
     1321 atttctgtta aaaccaataa ttcatttgta ttcaaaccat attttttaat taataatttt
     1381 aagttttttg gaaacaaatg cacatattca acaccttcgg aaatagattt aaatttattt
     1441 tcctttgttt ccgaaataac taaagtctta tttttcttag acgctttcgc gtgaaattca
     1501 taaacttcta ctttttgctc aggtgttaaa tcatactttt ccaaaaacaa atctaatttt
     1561 gaatattcaa cattcaaact ctcatttaat atatttccaa tatccataga aacctcctct
     1621 tttttattta tttctatata tatgttttaa catttataaa ggactagtca atagattgag
     1681 ttgcaaaagg tagaaaaagt ttcagttttg aaactgtagt ttctacttgg aaactggcta
     1741 gagttgtcgg atttgacaac ctcagttgac gaatttgaca actagagttg acgaatttga
     1801 caactacggt tgaagttttt gacaactgcc ttttttaaaa agtcagtaat atcaatggtt
     1861 agagagtagt tttttaactc ctaagaacat ctaagaattt taagaacact aagggggtga
     1921 aattttcaac ttttgagatg gcttttaaga tcattggttt tcaagtaaca gatcaatccc
     1981 ccacggggga aaaccatcca gttacccggt tccgggcttc tgcttcgcta tggaggattt
     2041 tgctgtaaaa ccgtcctgcc ggacgggcca acccttcaca gtccaggagg gaacctcctg
     2101 aactgctcac ggttcacatt ttgaagcgac gaacgggagc cggtggagga ctgctggggg
     2161 tggaagtatc ggcaattttt gccgctgctt tgtttttatt tgcgatctta aatctcaata
     2221 atctatctcc gccacggggt ttaacattgg tttcgacatc tgcgatgtca tcaaatccac
     2281 ctttgctttt tttgctcttt cttccgtaac tctgctgaga tctaactgag gcatggccca
     2341 taatttgagc
//
