LOCUS       NZ_CP054352             1822 bp    DNA     circular CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-176 plasmid pSCU-176-7, complete
            sequence.
ACCESSION   NZ_CP054352
VERSION     NZ_CP054352.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14943547
            Assembly: GCF_013315675.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1822)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Hartman,A., Gonzalez,A.,
            Gill,M., Pandori,M. and Hess,D.
  TITLE     Title: F plasmids are the major carriers of antibiotic resistance
            genes in human-associated commensal E. coli
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 1822)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Hartman,A., Gonzalez,A.,
            Gill,M., Pandori,M. and Hess,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-MAY-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                   :: 100x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 03:58:56
            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)                     :: 4,962
            CDSs (total)                      :: 4,848
            Genes (coding)                    :: 4,620
            CDSs (with protein)               :: 4,620
            Genes (RNA)                       :: 114
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 228
            CDSs (without protein)            :: 228
            Pseudo Genes (ambiguous residues) :: 0 of 228
            Pseudo Genes (frameshifted)       :: 88 of 228
            Pseudo Genes (incomplete)         :: 149 of 228
            Pseudo Genes (internal stop)      :: 51 of 228
            Pseudo Genes (multiple problems)  :: 52 of 228
            Pseudo Genes (short protein)      :: 3 of 228
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054352.1.
            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..1822
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-176"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-176-7"
                     /geo_loc_name="USA: California"
                     /collection_date="2017"
     gene            complement(join(1299..1822,1..10))
                     /locus_tag="HPE52_RS24560"
                     /old_locus_tag="HPE52_24550"
     CDS             complement(join(1299..1822,1..10))
                     /locus_tag="HPE52_RS24560"
                     /old_locus_tag="HPE52_24550"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /GO_process="GO:0006260 - DNA replication [Evidence IEA];
                     GO:0006276 - plasmid maintenance [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="replication/maintenance protein RepL"
                     /protein_id="WP_000893324.1"
                     /translation="MLEQQFEDFEQQKRRDHQAQDQSKSAKQKRDRLNPPDWSQVTKAG
                     WNMLDSISEKVPRAFRLYSFFAQNIDKSCGAVVCDQKFLADYFGVSLRTIQYWIGDLES
                     IGAIVKIPVGIYYAYALDPYQVWRGYNKSKKYAAFNAKTLTQKDGVIDRKLRLMLSRRE
                     EFEGSLKTSNHDLD"
                     /name="replication/maintenance protein RepL"
     gene            complement(999..1286)
                     /locus_tag="HPE52_RS24565"
                     /old_locus_tag="HPE52_24555"
     CDS             complement(999..1286)
                     /locus_tag="HPE52_RS24565"
                     /old_locus_tag="HPE52_24555"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001220925.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_023909281.1"
                     /translation="MRIKYESRWKLEELKLEICRSIDSLIDEYHIEYAMGINLYMNCED
                     KEFNPVDIVNEDGKNIMFVVSNNEKIQKPKKSAKKKIPAPVIELDKYRKK"
                     /name="hypothetical protein"
     Typing          497..748
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.885"
                     /coverage="97.0"
                     /evalue="1.85e-99"
ORIGIN
        1 gttccagcat acttgcatcc ttacctgcaa cgttgtttcg caccttacga aatttatatc
       61 gtacattacg aaacaacaca cgcaaacatg tttgcgtata cacatgcaaa taacgtttcg
      121 tatgttggtg tcataatgct ttgattttta agagaatgtc gatttttgct ctaaagatct
      181 atcaaagcac ttttttgcta cacaagattt aattagttca tcgaacattt ggggtgtcgg
      241 ggcgaagccc tgacccagtc acgtagcgat agcggagtgt atactggctt actcttctgc
      301 aagcctcgcc agccgtgatt ttgcccgatt tcgcgctctc cacgttcaac agctcgatca
      361 tgtttttgca gtccgttcac cgctaaaacg ccccgcatca gtgcgtacgt gctcaatgtg
      421 gtttccggtt ctcttccgct tcctcgccca ctcgctcact aacgttcggt cgctggggct
      481 gcggcgagcg gtgccacctc tcgcatgtta tcggtgattc cgctgttgtt ctttcgggga
      541 tgagtcgcca gatagctctt caaacgctct cagaagctct cagacgcacg aaacgggttt
      601 taaatgccca tcagggcatg gaaggcgcga aaaacgctta cagagggttt taggaggtca
      661 ggcgcgccga tacccctaac caggggattt caggtcgcca ggaaccgcgt cagccccctg
      721 caaagcccat ttgcacggaa taggcagcca cgcggttggt aggtggtcgt agaccgtcga
      781 tgttacagcg atgggggtct ggggttctcc ccagacggtt tccggttgcg ctcaaggcgc
      841 tgccggaacc gtggcggctc ggtcgttctg gaaaacgggg agcaaaaaga cgcaagggat
      901 tttgaggcgg caaaagagca atgcaggata gacaatcaac tagaaattgc atgcaatgtt
      961 ctgtggattg tccgcctgcc gctggctctg tatggccatc actttttccg atatttatct
     1021 aactcaatta caggtgcagg aatttttttc ttcgcacttt tttttggttt ttgtattttt
     1081 tcattgttgc taacaacaaa cataatattc tttccatctt cattgacaat atcaacggga
     1141 ttaaactcct tatcttcaca attcatatat agatttattc ccattgcata ttcgatatga
     1201 tattcatcaa ttaacgaatc tattgatcta catatttcta attttagttc ttctaatttc
     1261 caacgtgatt catatttaat tctcatagcg catcatacct agtccaagtc atgattagat
     1321 gtcttaagcg agccttcaaa ctcttctctc ctagagagca tgagccgcaa cttgcgatca
     1381 ataacgccat ctttttgagt taatgttttt gcgttaaacg ctgcatattt tttagattta
     1441 ttatatccgc gccatacctg atacggatct aacgcataag cataatagat acctactggt
     1501 attttcacga tggcaccaat actttctaaa tctccaatcc aatattggat cgtccttaaa
     1561 ctaacaccga aataatcagc taagaatttt tggtcacata caacagcccc acacgattta
     1621 tctatatttt gagcaaaaaa agaatatagc ctaaatgctc tgggaacctt ctcagatata
     1681 gagtccaaca tattccagcc cgccttagta acctgcgacc agtcaggtgg attcaaccga
     1741 tctcgttttt gcttagcact tttggattga tcttgtgcct gatgatctcg ccgtttttgc
     1801 tgttcgaaat cttcaaattg ct
//
