LOCUS       NZ_CP053255             2113 bp    DNA     circular CON 14-JUN-2023
DEFINITION  Escherichia coli strain SCU-204 plasmid pSCU-204-4, complete
            sequence.
ACCESSION   NZ_CP053255
VERSION     NZ_CP053255.2
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14609789
            Assembly: GCF_013085905.2
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2113)
  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  JOURNAL   Unpublished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 2113)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Hartman,A., Gonzalez,A.,
            Gill,M., Hess,D. and Pandori,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-JUN-2020) Biology, Santa Clara University, 500 El
            Camino Real, Santa Clara, CA 95054, USA
  REMARK    Nucleotide sequence updated by submitter
REFERENCE   3  (bases 1 to 2113)
  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                   :: 155.0x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/14/2023 04:36:16
            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)                     :: 5,285
            CDSs (total)                      :: 5,165
            Genes (coding)                    :: 4,920
            CDSs (with protein)               :: 4,920
            Genes (RNA)                       :: 120
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 245
            CDSs (without protein)            :: 245
            Pseudo Genes (ambiguous residues) :: 0 of 245
            Pseudo Genes (frameshifted)       :: 97 of 245
            Pseudo Genes (incomplete)         :: 157 of 245
            Pseudo Genes (internal stop)      :: 46 of 245
            Pseudo Genes (multiple problems)  :: 51 of 245
            Pseudo Genes (short protein)      :: 4 of 245
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP053255.2.
            On Apr 28, 2021 this sequence version replaced NZ_CP053255.1.
            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..2113
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-204"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-204-4"
                     /geo_loc_name="USA: California"
                     /collection_date="2013"
     gene            join(1964..2113,1..816)
                     /locus_tag="HHJ42_RS25125"
                     /old_locus_tag="HHJ42_26135"
     CDS             join(1964..2113,1..816)
                     /locus_tag="HHJ42_RS25125"
                     /old_locus_tag="HHJ42_26135"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012421200.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="WP_001287824.1"
                     /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQTAAEFERYALRMA
                     SCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIVVD
                     YPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRGKDG
                     SAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGEVVAN
                     VAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQLDRETN
                     EDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD"
                     /name="protein rep"
     gene            820..1086
                     /locus_tag="HHJ42_RS25130"
                     /old_locus_tag="HHJ42_26140"
     CDS             820..1086
                     /locus_tag="HHJ42_RS25130"
                     /old_locus_tag="HHJ42_26140"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001024536.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001024536.1"
                     /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTFG
                     FHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS"
                     /name="hypothetical protein"
     Typing          245..476
                     /name="Col(BS512)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.05e-118"
ORIGIN
        1 ttacgttttg gttggtctac catcatggaa accggagaaa cgcgcctacg gcttcgtagt
       61 gcgcaatttt gccgtgtccg tcattgccct gtctgccagt ggagaagaac cctcatgtgg
      121 caagcccgtt tttatcaggc tctaccgaaa atcgttgtgg attacccgtc ttcccgatgg
      181 ttgtttctga cgttaactgt caggaactgc gagataggtg aacttggaac agtccttaca
      241 gcaatgaatg cggcgtttaa gcgaatggaa aagcgaaagg agctatcacc tgttcagggg
      301 tggatcaggg ctacggaggt gacgcgaggt aaggatggca gcgcacatcc gcattttcac
      361 tgtctgctga tggtgcaacc ttcttggttt aaagggaaga actacgttaa gcacgaacgt
      421 tgggtagaac tctggcgcga ttgcttgcgg gtgaactatg agccgaatat cgatattcgg
      481 gcagtaaaaa ctaagacagg tgaggttgtg gccaacgttg ccgagcaact gcaaagcgcg
      541 gttgctgaaa cgctgaaata ctccgttaaa ccggaagata tggcaaacga tcctgagtgg
      601 tttcttgagc tgacgcggca gcttcacaag cgccgtttta tctcgaccgg tggggcgcta
      661 aaaaacgtcc tccagttgga tcgagaaacc aatgaggatc ttgtcattgc cgacgatgta
      721 ggggatggca ctgatgacgg gaagcggacg gcgtttgtct gggattcagg taaacggcgt
      781 tacaaacgcg cccctgagaa ggataaatcg gattaacgta tgaatattaa tattgaatac
      841 ctgaatggaa ataagactat tggtttattt tttttaagaa gtgaagcggt gattcctgac
      901 aggtttaaaa accttatttt gcttattgat ggattaagtt ttggcacatt tggttttcat
      961 ccgcacgaag gttttgagga tgaattaatt ttatatattc agaaaacaaa cgagagggta
     1021 aaaactcttt ttgtgaaaat agatttaaac ggtatcaagt ttggattttt aagaacgcat
     1081 tcttagttct ggaaaagagc cagcggcagg ctgaggtgat aggtacgaga ttgcatgcaa
     1141 tctctagtgc tctgtctatc ctgcattatc ctcagcatta tcctcagcat tatcctcagc
     1201 attatcctca gccttgccaa ctcgacacca atgcaggata gacaatccga tgtcaaatgt
     1261 taacactctg cgagtggtac attttccccg gattatcgtc ctgagcctgc cgctggctct
     1321 ctttctaccg cctcgctttg ctcgttgctc aacgcctcac agacacggat taaaatccgc
     1381 atccgttcac cgttttttaa agtccgttaa aagcatgatg ccatctccga gagttaatct
     1441 cgtcaaatgc taaatcgtgg gggtcccctt tggggttccg atttagtgat tgacgacacc
     1501 accgattaaa aaacttatgc ggggtggatg gtttcacgaa gtgaggccat ccacctgtaa
     1561 gacagggttt tgtttttatt ccctgttttg gtgatcgggt gtgtggaaaa ggttggggta
     1621 agccgttcgg gggtgcttgt tttggggggt taaaattgtg gttatttttt gcgcaattct
     1681 cgcgcgtgat ccttgtattt atacttaagg gataaatggc ggatatgaaa tagtggttta
     1741 gcccagtaat gacgaggctt tgagtgggtt ttgacaggtc aaagaaaatg gagcagaatt
     1801 gaggcgtttt taatcggcgt tggggagtgc gtcaacactc cccaacattt cgaatgtgtc
     1861 acctcagcgg caaactctgg tgacatgtac tggctcgcaa tgcacaggta cgtgatgaat
     1921 ataccacatc aaatcacagc ctgcccagat cggagcaggc ttaatgtcag aagataaatt
     1981 cctttcggac tacagccccc gtgatgcagt ttgggatacc cagcgcacgc ttaccgattc
     2041 tgtcgggggt atctaccaga ctgctgctga attcgagcgc tatgcactcc gtatggcctc
     2101 ctgtagcggt ttg
//
