LOCUS       NZ_CP060078             4197 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain G3/10 plasmid pSYM2, complete sequence.
ACCESSION   NZ_CP060078
VERSION     NZ_CP060078.1
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 4197)
  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  JOURNAL   Unpublished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 4197)
  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
            CP060078.1.
            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..4197
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="G3/10"
                     /isolation_source="feces from healthy individual"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSYM2"
                     /geo_loc_name="Germany"
                     /collection_date="1954"
     gene            complement(join(4183..4197,1..1125))
                     /gene="dcm"
                     /locus_tag="H4P47_RS24820"
                     /old_locus_tag="H4P47_24820"
     CDS             complement(join(4183..4197,1..1125))
                     /gene="dcm"
                     /locus_tag="H4P47_RS24820"
                     /old_locus_tag="H4P47_24820"
                     /EC_number="2.1.1.37"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000131511.1"
                     /GO_function="GO:0003886 - DNA
                     (cytosine-5-)-methyltransferase activity [Evidence IEA]"
                     /GO_process="GO:0006304 - DNA modification [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA (cytosine-5-)-methyltransferase"
                     /protein_id="WP_000131512.1"
                     /translation="MTDNIAATIKGKRERLHMTQKEFADALGLSKYGDRTIRRWERGET
                     KPTGAELKAVMDFPDTPPYPNNENGRYRMIDLFAGIGGTRLGFHQTNAVNVVFSSEWDK
                     FAQKTYHANYGDFPDGDITKIDEKDIPDHEILVGGFPCVAFSQAGLKKGFNDTRGTLFF
                     DIARIIKEKKPHAFLLENVKNLLGHDKGRTFSIIKNTLEELNYTVYYNIFAAKDFGVPQ
                     NRERIYIVGFNKEKVRNHEHFTFPTPLKTKTRVGDILEKSVDNKYTLSDALWNGHQRRK
                     LVNAAAGKGFGYGLFNENSPYTNTISARYYKDGSEILIEQKGSNPRKITPREASRLQGF
                     PSDFIIPVSDTQAYKQFGNSVAVPVINAIAEKIISTLDS"
                     /name="dcm"
     gene            1196..2152
                     /locus_tag="H4P47_RS24825"
                     /old_locus_tag="H4P47_24825"
     CDS             1196..2152
                     /locus_tag="H4P47_RS24825"
                     /old_locus_tag="H4P47_24825"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014640333.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0009036 - type II site-specific deoxyribonuclease
                     activity [Evidence IEA]"
                     /GO_process="GO:0009307 - DNA restriction-modification
                     system [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type II restriction endonuclease"
                     /protein_id="WP_223152166.1"
                     /translation="MKKLSSRYKRLFFMQRLSPGEFKTLISKERKSHFITPFALVHKTF
                     CDLGYDQKNSDYFLNNPSEYIIAMRKNCWKEFEPFEKEFTTRMLSYLIDEERIKDMSPY
                     DAIRDFTMEYPTHIYDLALSNTQSRRSRAGKEFESILELLMMGAGIPVDVQGAIGKSFF
                     QKNQIGKLVDLVMPGVVQYTSNKRNTMLISAKTTLRERWQEVPEEVNRTGIREMYLATL
                     DDSFSEETINILYEANVVVVTTIENKNFKYKNNNRVLTFEDMLQSAMELSRKWNNVSYT
                     DSEKEEIQQSILKQIEKYSDFPYVVNYYRNRLSALVD"
                     /name="type II restriction endonuclease"
     gene            complement(3170..3364)
                     /locus_tag="H4P47_RS24830"
                     /old_locus_tag="H4P47_24830"
     CDS             complement(3170..3364)
                     /locus_tag="H4P47_RS24830"
                     /old_locus_tag="H4P47_24830"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041627.1"
                     /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_001041631.1"
                     /translation="MNKQQQTALNMARFIKSQSLTLLEKLDALDADEQAAMCERLHELA
                     EELQNSIQIRFEAESETGT"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          3003..3087
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="3.03e-37"
     Typing          3401..3499
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.0"
                     /coverage="100.0"
                     /evalue="1.35e-41"
     Typing          3624..3879
                     /name="MOBF"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.899"
                     /coverage="89.0"
                     /evalue="2.61e-118"
     Typing          complement(2434..2979)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.989"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 cgatatgatt ttttctgcta ttgcattgat aacagggact gcgactgaat tcccaaattg
       61 cttataagcc tgtgtatccg atacagggat aataaaatca ctaggaaacc cttgaagtct
      121 tgacgcttcc cgcggagtta tttttcttgg gttacttcct ttttgctcta ttaatatttc
      181 gctaccatct ttatagtacc tcgcacttat ggtattagta tatgggctat tttcattaaa
      241 taaaccatac ccaaagcctt taccggctgc tgcatttaca agtttcctgc gttggtgtcc
      301 attccagagc gcatctgata gcgtatattt attgtctacg ctcttttcaa gaatatctcc
      361 aactcttgtt tttgttttta atggggttgg aaaagtaaaa tgttcatgat ttcttacttt
      421 ttctttatta aagcctacaa tgtatatgcg ttctctattt tgtggaacac caaagtcttt
      481 tgcagcgaag atattgtaat acacagtgta attcaattct tcaagtgtgt tttttattat
      541 tgaaaaagtt ctacctttat catgtcctag caagtttttt acattttcaa gtaaaaaagc
      601 atgaggtttt ttttccttta ttatccttgc tatatcaaaa aacaaagttc ctcttgtatc
      661 attaaatcct tttttgagcc ctgcttgaga gaatgctacg caaggaaacc caccgacaag
      721 aatttcatga tcaggaatat ctttttcatc gatttttgtt atgtccccat cagggaaatc
      781 accataattt gcatgatatg tcttttgagc aaacttatcc cattcgctgg aaaaaacaac
      841 atttacagcg ttagtttgat gaaatccaag tctggttcca ccgattccag caaataaatc
      901 gatcatgcga tatctgccat tctcgttgtt tgggtaaggt ggtgtgtctg gaaagtccat
      961 aactgctttt agttccgccc cagtaggttt tgtttccccg cgctcccatc ttcttatggt
     1021 tctgtctcca tattttgaaa gaccaagggc gtctgcaaac tctttttgag tcatatgaag
     1081 tctttctctt tttcctttga ttgttgctgc gatattatca gtcatgcatg tctaccagaa
     1141 ttaagtgttg gttttaggac aatttgtcct gttttgattc caattatgaa cgtgcatgaa
     1201 aaaactttca agtagatata aaaggttatt ttttatgcaa agattgagtc ctggtgaatt
     1261 taaaactcta atttctaaag agagaaagtc gcattttatt acgccatttg ctttggttca
     1321 taaaacattt tgtgatttag ggtatgatca aaaaaatagt gattattttt tgaataatcc
     1381 aagtgaatat ataattgcaa tgaggaaaaa ctgttggaaa gaatttgaac catttgaaaa
     1441 agaattcaca acaagaatgt tatcatatct tattgatgaa gaaagaataa aagatatgag
     1501 tccttatgat gccattcgtg attttacgat ggaataccct acacacatat atgatttggc
     1561 actgtctaac actcaatcca gacgtagcag ggcaggaaaa gagtttgagt ctattcttga
     1621 gctattgatg atgggggcag gaattcctgt tgatgtgcag ggggctattg ggaagtcatt
     1681 ttttcaaaaa aaccaaatag gtaaacttgt agatcttgtt atgccaggtg tagtccagta
     1741 cacatctaac aaaagaaata caatgttgat ttccgctaaa acaacgctga gggagcgatg
     1801 gcaagaagta cctgaagagg ttaatagaac aggaattaga gaaatgtatc tagctacact
     1861 agatgattct tttagcgagg agacaataaa tatattatac gaggctaatg tggtcgttgt
     1921 aacgacgata gaaaataaaa atttcaaata taaaaataat aatagggtgc taacctttga
     1981 agatatgcta cagtcagcaa tggaattatc aagaaagtgg aataatgtaa gttacacaga
     2041 ctctgaaaaa gaggaaattc aacagtcaat attaaaacaa atagaaaaat atagtgattt
     2101 cccttatgtt gttaattatt atagaaatag gcttagtgct cttgttgact aaaaaactaa
     2161 aaggatctct tgagatcctt tttttctgcg cgtaatcttg gacctgtaaa cgaaaaaacc
     2221 accctggcag gtggtttttt cgaaggttag ctaatcctgg cagattatct aaccgaggta
     2281 atctggcttc agcagagcac agataccaaa tactgtcctt ccagtgtagc cgtagttagg
     2341 ccatcacttc aagaactctg taagcatctg gataaatctc gctctgctaa tccggttacc
     2401 agtggctgct gccagtggcg ttaaggcgtg tcttactggg ttggactcaa gacgatagtt
     2461 accggataag gcgcagcggt cgggctgaac ggggggttcg tgcacacagc ccagcttgga
     2521 gcgaacgacc tacaccgggc cgagatacca acagcgtgag ctatgagaaa gcgccacgct
     2581 tcccgaaggg agaaaggcgg acaggtatcc ggtaagcggc agggtcggaa caggagagcg
     2641 cacgagggag cttccagggg gaaacgcctg gtatctttat agtcctgtcg ggtttcgcca
     2701 cccctgactt gagcgtcgat ttttgtgatg ctcgtcaggg gggcggagcc tatggaaaaa
     2761 cgccagcggc gcggcctttt gttgcccttt gcctttttac gcacatgttc tttccggcct
     2821 tatcccctga ttctgtggat aaccgtattt ccgcctttga gtgagccggc accgcttgcc
     2881 gcagccgaac gaccgagcgc agcgagtcag tgagcgagga agcggaagag cgcctgatgc
     2941 ggtatgttct ccttacgcat ctgtgcggca tttcacaccc ggcatggcgt gcttttcata
     3001 caatccgcac tgatgccgca tagttaagcc agtatacact ccgctatcgc tacgtgactg
     3061 ggtcatggct gcgccccgac acccgctaaa accccctgac gcgccctgac gggcttgtct
     3121 gctgacgaaa acgcccacgg gaaagccgtg accgcctccg tcagcttcgt tatgttcctg
     3181 tttcactttc ggcctcaaag cgaatctgga tgctgttctg gagttcttct gcgagttcgt
     3241 gcagtcgttc gcacatggcc gcctgttcgt cggcatccag agcatccagt ttttcaagca
     3301 gtgtcaggct ctggcttttg ataaatcgcg ccatattcag cgcagtttgt tgttgtttgt
     3361 tcaccttcct ttgttctccg tcagttccgg gtgtcggggg gaccctgagc aggtggtaat
     3421 tgtaagacgt tgcgggcgac ggtattacaa ttgcacatcc tgtcctgttt ctttaggacg
     3481 tatcatggca cagcatatca actgataaat aatccctgtg cagtgcagcc gctgttgcat
     3541 aaaatttcgc tctgcgtcga gtgtttctta atcaataatt ccgctgatac tccggaaaaa
     3601 cgcgagtctg ttctcatgcc tgaaatgccc acaccccacg caaaaacaag tttttgctga
     3661 tttttcttta taaatagaga gttatgacaa attagttctt cttgctctct ttgtgatatt
     3721 taaaaaagcg gtgtcggcgc ggtgttgtag ctgcgccaac accgcttttt aggggtggta
     3781 ctgactattt tcataaaaaa catcatctta tattaggggt gctgctagcg gcgcggtgtg
     3841 tttttttaca ggacacccct gggggcgctg ctaggggtgt ctgttcagat atgtagcaat
     3901 gagtcaggga ttcacgaact gaaaatgtcc gaaaatgtgt ctcatgggca ctgtatgcgc
     3961 ccaaaccgat cgtcattcac tttcatgcat agctatgcag tgagctgaaa gcgatcctga
     4021 cgcatttttc cggtttaccc cggggagaac atctcttttt gcggtgttcg cggcagaatc
     4081 gctttcagcg cgttttagcg gtgcgcgcaa tgcgacgtta tggtaaatcc atatgggggg
     4141 gggaattgga ttctgggccg cattgtgtcc ttatgactta gtttatgaat ctaaggt
//
