LOCUS       NZ_CP053243             3863 bp    DNA     linear   CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-106 plasmid pSCU-106-9, complete
            sequence.
ACCESSION   NZ_CP053243
VERSION     NZ_CP053243.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14609771
            Assembly: GCF_013085185.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3863)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Gonzalez,A., Gill,M.,
            Hartman,A., Pandori,M. and Hess,D.
  TITLE     F plasmids are the primary drivers of antibiotic resistance in
            human-associated commensal E. coli
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3863)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Gonzalez,A., Gill,M.,
            Hartman,A., Pandori,M. and Hess,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (17-APR-2020) Biology, Santa Clara University, 500 El
            Camino Real, Santa Clara, CA 95054, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 14x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 03:10:47
            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)                     :: 5,452
            CDSs (total)                      :: 5,328
            Genes (coding)                    :: 5,059
            CDSs (with protein)               :: 5,059
            Genes (RNA)                       :: 124
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 269
            CDSs (without protein)            :: 269
            Pseudo Genes (ambiguous residues) :: 0 of 269
            Pseudo Genes (frameshifted)       :: 108 of 269
            Pseudo Genes (incomplete)         :: 154 of 269
            Pseudo Genes (internal stop)      :: 52 of 269
            Pseudo Genes (multiple problems)  :: 47 of 269
            Pseudo Genes (short protein)      :: 3 of 269
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP053243.1.
            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..3863
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-106"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-106-9"
                     /geo_loc_name="USA: California"
                     /collection_date="2015"
     gene            1070..2068
                     /locus_tag="HHJ24_RS26935"
                     /old_locus_tag="HHJ24_26930"
     CDS             1070..2068
                     /locus_tag="HHJ24_RS26935"
                     /old_locus_tag="HHJ24_26930"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016237859.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_062861057.1"
                     /translation="MKNPELKNLTDYSPEDKPWDERRSFSDDVGGIYLRAAGFEHYGER
                     VGACSGILRFGWSTNTETGETRLRLRDARFCRVRHCPICQWRRSMMWQARFYQSLPKIV
                     AEYPGARWLFLTLTVRNCSIDALGETLTAMNAGFLNLKRRKEFRGVLGWVRTTEVTRGK
                     DGSAHPHFHTLLMVSPSMLSGREYVKHARWVELWRDCLRVAYDPNVDIRVVKSRKPKDD
                     ESLPCAVAEQLRGAVVETLKYSTKPADMLADPEWFLELTRQVHKRRFVATGGALKNVLQ
                     LERETNEDLIMADGMAEGTDDGSRLAFSWVPVVKKYQRDRAKDKRRLSSDD"
                     /name="protein rep"
     gene            complement(2051..2488)
                     /locus_tag="HHJ24_RS26940"
                     /old_locus_tag="HHJ24_26935"
     CDS             complement(2051..2488)
                     /locus_tag="HHJ24_RS26940"
                     /old_locus_tag="HHJ24_26935"
                     /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_136763429.1"
                     /translation="MAVAASARNALKIIRCTANKKLSSTKNHVKTIASTFLSPSITVKH
                     SASVGKLLTSIIQFLIDNNSGDIPSFEGLFLPTHHKQHPYHRQNRAQNVSDGLNQPKHI
                     KPLPDAKNRVRKRLSAFLESKKLSAVDFHCRDPETRSIIAA"
                     /name="hypothetical protein"
     gene            complement(3124..3351)
                     /locus_tag="HHJ24_RS26945"
                     /old_locus_tag="HHJ24_26940"
     CDS             complement(3124..3351)
                     /locus_tag="HHJ24_RS26945"
                     /old_locus_tag="HHJ24_26940"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016237860.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_062861059.1"
                     /translation="MSVDVIKQIQSIQDKGIIIYSKYRANEFDRDDVYRESYTLIIEFN
                     HLIAEHAVHDEKLINHTVCILNELRSIAIN"
                     /name="hypothetical protein"
     Typing          2636..2713
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="96.25"
                     /coverage="87.0"
                     /evalue="2.63e-28"
     Typing          complement(1788..1977)
                     /name="Col(MP18)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.476"
                     /coverage="99.0"
                     /evalue="1.71e-93"
ORIGIN
        1 cgctccagtc tgacagcttc gtttgcgggt gaaaaatatt tattttctaa ataaattgct
       61 ttgtcctgat tcatactcgt aatttatatt tttatttgaa ttaaaaaaga gcggcctgtc
      121 gggttaatac atattggcat gactgttgat atatcagccc aacagcacgc tcgtaatcgt
      181 tttaacgtga ttttcgcaac atggcaatcc gggttcatct gtccggtaat caataaaaac
      241 cgtgcgaaaa acgggacagg atgtgtattt gtcggaccgc gcacacgcaa tcagacaaat
      301 gccgcctggt caggactgcg ccccgacacc ccgccaacgt ctcacgcagc cagattgaaa
      361 tctgtcagcg ttcgccgttt tctgactcgt caaacagaaa atcgtggggt cccgcgcctc
      421 cggcgtgggt tccgattttg tgattgacga cggtacgaga aaaaatactg gtgatggtgg
      481 ttggtgtcac gcagtgaggc caaccacctg caaagcgggt ttttaggagg atgggaattg
      541 aaaaatatct atcagctata cgaggaaaat tgcaacagag tcggatttaa ggttcggcgg
      601 acatcatggg ggagaactgt tgcggttatt aaatccattg gtgggaagac tcgcgggaag
      661 ctttcgggtt atgcgcctta ctacggtaat caaagggttg tggctgagat tcatacgccg
      721 agtggtgtta ttacggatgt tctttcgtgt gctgggtgct accagtggga gctcgtggat
      781 tgatgcgttt ttaggtggtc gccaccttgt atatatactt aagggataaa tcgacaactc
      841 gaaatcatgc tctaggcctt gtcacgactg gcctgaacgt ggatttgcgt ggaaataggt
      901 ttgagagtat tttgtcggaa gtggtcgcat taaaagcgac ccccgcaacg atgggcgtcg
      961 ttcgggggtg tgaccacctg taggaattcg aattggtgac acgacaacac aggtgataca
     1021 ggaatgataa cacgtaattt cgtctgtcgc tcactaggga acggcagaca tgaaaaatcc
     1081 tgaacttaaa aatctgacgg attattcccc ggaggataaa ccgtgggatg agcgccggag
     1141 cttttccgac gatgtgggcg gtatttatct gcgtgctgcc ggatttgagc actacggcga
     1201 acgtgtcggg gcttgtagtg gtattttgcg gtttgggtgg tcaacaaaca cagagaccgg
     1261 agaaacgcgt ctgcggttgc gtgatgcgcg gttctgtcgt gtccggcact gtccgatctg
     1321 ccagtggagg cgctccatga tgtggcaagc ccgtttctat cagtccctgc caaagattgt
     1381 ggcggaatat ccaggcgcgc gctggttgtt tctcacgctg acggtgcgca actgttccat
     1441 tgatgcgctt ggtgagactt tgaccgcgat gaatgcgggt tttttgaatc tcaagcgtcg
     1501 caaggagttt cgtggtgtgc tgggctgggt tcgtaccacg gaagtaacgc gcggcaagga
     1561 tggtagcgca catccccatt ttcacactct gctgatggtt tccccctcga tgttgtccgg
     1621 ccgtgagtat gtgaaacatg cccgttgggt ggaactgtgg cgtgattgtc tgcgggtggc
     1681 gtatgacccg aatgtggata tcagggtggt gaagtcacgg aaaccgaaag acgatgaatc
     1741 tttaccttgt gctgttgcgg agcagctgcg cggcgcggtg gttgagactc tgaaatattc
     1801 cacaaagcct gctgatatgc tggctgatcc tgaatggttc ctcgaactaa cacggcaggt
     1861 acacaagcgt cgttttgttg ctacgggggg agcgcttaag aacgttctgc aactggagcg
     1921 ggaaacgaac gaggatttaa tcatggcgga tggcatggca gagggtacag atgacggttc
     1981 ccgtctggcg ttttcgtggg tgccggttgt caaaaaatac cagcgcgatc gggcgaaaga
     2041 taaacgtcgg ctaagcagcg atgattgagc gcgtttctgg gtctctgcaa tggaaatcca
     2101 cggctgacag ctttttgctc tccagaaacg cactcagacg ctttctaacg cgattttttg
     2161 catctggcaa tggttttata tgttttggtt gattcaggcc gtcagagacg ttttgagcgc
     2221 gattttgacg atgatatgga tgctgtttgt ggtgtgtggg taaaaaaagc ccctcaaaag
     2281 aggggatatc accggaatta ttgtcaatga gaaattgaat tatggaagtg agcaacttcc
     2341 cgacagatgc agaatgtttg accgtaattg aaggagacag gaaggtgctc gcgattgttt
     2401 taacgtgatt ttttgtagat gacaattttt tgttcgctgt acatctgatg attttgagcg
     2461 cgtttctggc gcttgctgct actgccaaac catccccatg gtcagttgat gccagaaacg
     2521 cgcaggagtt ttgtagcgcg tctccggtcc ctaatcaatg aattcccggt cattaacatg
     2581 cgtttacccg gaaacgcgcc ctgatgttct atcgtattgc gggaactgtg tcgagggtgt
     2641 cgggcaaagc cctgaccagg tggtaatcgt atatccgtgc gtgcgcggtt atacgattac
     2701 acatcctgtc ccgaaatcag gattgttttt cacgtacaac tgcggcaaat tcaccccgtt
     2761 gcggttgcaa cgatgggaat atcaaaacta cgaaaattat ttagccattt gctacccctc
     2821 tggccctggc ctccaccagt tccggggggg ggattttttt gttgcctctc atgacgaact
     2881 acggcaaatt tctgacgttg caaactgcaa cacataaaac acacaaaact cacaaaactc
     2941 acaattgcca tgtcctcatt gacaccccct tgccatatag ggggattttt tcgcctgtcc
     3001 tgattgtctt ttgctgatgg ttacggcaga ttggaaaaga gcgcatttgt ggtgctctct
     3061 ccaaaataat atttttcatt actcaaactc tgatggcttc cccctgtaat ccagggggat
     3121 tttttaattt atcgctatgc ttcgtaattc attcagaata cagacagtat gattaatcag
     3181 tttttcatca tgaacggcat gttcagcaat aagatgatta aactcaataa tcagggtgta
     3241 actctccctg tatacatcat cccggtcaaa ttcatttgct ctgtattttg aataaataat
     3301 aattcctttg tcctgtatgc tctgaatttg tttaattaca tcaacactca taaaaacacc
     3361 caataaaaca gataacagat gccagaagca aacatcacaa aacataccaa agacgtcatt
     3421 ttgcggtgtt tgccctatcc tgcatcagaa cgctaaaaac aggaatctct ttatgacgaa
     3481 tcctccattt caggattttt tatgtagcgt ctactacatg cgatccgttg gtgagttcgt
     3541 ttggcgcaga cccaatattt agtgcttatt agtgctcatt agtgattatt aatgcgtatt
     3601 agtgcgtatt agtgattatt gattgttaag agtccgcggt tgctgaaatt ctggaggcac
     3661 gttaccgact gtatacaaaa tgctggcgca ttttgatacg tcgacgtgcc aaaggggacg
     3721 cccctttgaa atcccgccag aattaaaagc ggcctgtctt tttacagtat tcagctctgg
     3781 ctatacacca gtctatattt tcgcctttgg cataatgaag cgcatcatgc cattttttcc
     3841 atgctccaat gtaatcacct tca
//
