LOCUS       NZ_CP053250             1538 bp    DNA     linear   CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-482 plasmid pSCU-482-3, complete
            sequence.
ACCESSION   NZ_CP053250
VERSION     NZ_CP053250.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14609798
            Assembly: GCF_013085025.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1538)
  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  JOURNAL   Unpublished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 1538)
  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                   :: 34x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 03:02:06
            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)                     :: 5,216
            CDSs (total)                      :: 5,099
            Genes (coding)                    :: 4,789
            CDSs (with protein)               :: 4,789
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 310
            CDSs (without protein)            :: 310
            Pseudo Genes (ambiguous residues) :: 0 of 310
            Pseudo Genes (frameshifted)       :: 188 of 310
            Pseudo Genes (incomplete)         :: 139 of 310
            Pseudo Genes (internal stop)      :: 43 of 310
            Pseudo Genes (multiple problems)  :: 58 of 310
            Pseudo Genes (short protein)      :: 4 of 310
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP053250.1.
            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..1538
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-482"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-482-3"
                     /geo_loc_name="USA: California"
                     /collection_date="2018"
     gene            <1..290
                     /locus_tag="HHJ51_RS25780"
                     /old_locus_tag="HHJ51_25780"
     CDS             <1..290
                     /locus_tag="HHJ51_RS25780"
                     /old_locus_tag="HHJ51_25780"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000469298.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=3
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_123004655.1"
                     /translation="EHIDPTCGAVVADQQFLAEKLGVSRSTIIRWLNYLESKNALVRIP
                     VAGKVCAYALDPHEVWKGYNTTKNHAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     gene            1352..>1538
                     /locus_tag="HHJ51_RS25785"
                     /old_locus_tag="HHJ51_25785"
                     /pseudo=""
     CDS             1352..>1538
                     /locus_tag="HHJ51_RS25785"
                     /old_locus_tag="HHJ51_25785"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000469298.1"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /name="helix-turn-helix domain-containing protein"
     Typing          895..976
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.795"
                     /coverage="100.0"
                     /evalue="6.23e-34"
     Typing          complement(1165..1273)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.95e-50"
     Typing          complement(523..780)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.769"
                     /coverage="99.0"
                     /evalue="1.81e-114"
ORIGIN
        1 cggagcatat cgatcctacg tgtggcgctg tcgttgcgga tcagcaattc ctagctgaaa
       61 aacttggagt tagcagaagc acaattattc ggtggctcaa ttacttagaa tcaaaaaatg
      121 cattagttag aatccccgtt gctggtaagg tttgtgcgta tgccctcgat ccacatgaag
      181 tctggaaggg atacaacact acgaaaaacc atgcagcgtt tgtcactaaa acactggtca
      241 acaaagacgg tgatattcag cgccgaatca tggccatgtt ttcaaattga gccagcggca
      301 ggcggacaat caggggctac gtgttaacgt tttgaccatg attgtctatc ctgcattgct
      361 cttttgccgc ctcaaaatcc cttgcgtgtt tttgctcccc gatccccaga acgaccgcgc
      421 cgccacggtt ccggctgcgc cttgagcgca accggaaacc gtctggggag aaccccagac
      481 ccccatcgct gtaacaccga cggtctacga ccaccaacca gccgaatagc tgcctgtgcc
      541 gtgcaaatag gctttgcagg gagctgacgc ggttcctggc gacctgaaag cccctggtta
      601 ggggtatcgg cgcgcctgac ctcctgagag cctctgtaag cgtttttcgc gccttccatg
      661 ccctggcggg catttaaacc cgtttcgtgc gtctgagagc ttctgagcgt gtttgaaggg
      721 ctatctgacg actcatcccc gaaagaacaa caacgggatc accgacaaca tgcgagaggt
      781 gatcccgctc gccgcaagtc gatgaccgag cgtagcgagc gaatcgacga ggaagcggaa
      841 gagaaccgga agttacattg agcacttacg cacggatgcg gggtgtcggg gtgaagccct
      901 gaccaagtgg ggaatgtctg agtgcgcgtg cgcggtccga cattcccaca tcctgtcccg
      961 atttctgagg cgttttaacg gtgaacggac ggcaaaaaca tgatcgagcg tggagagcgc
     1021 gaaatcgggc aaaatcacgg ctgacgaggc ttgcagagga gtaagccagt atacactccg
     1081 ctatcgctac gtgactgggt cagggcttcg ccccgacacc ccaaaagggc gttgcgttgc
     1141 gcgcaacgcc cttgcctaga atagatcttt tacgccgatt tgtaagttgt tgttttttta
     1201 gtgtgttttt tgtttacctg tcgcatccag ggtgacacaa cgttgtcgca tccaggatgc
     1261 gacaacacgc aacaaggtgt tgcacagatg tgtcatgatg gcttagattt gaaccaacgt
     1321 tagtgcatgg gattttcaga gggaaaaaat catgtttatt gattcagaaa aacgactgaa
     1381 acaactttca gatgaggcaa agaaaaacac cgaggatctc gaagaagcaa agaagaattc
     1441 aaggtttaca caggtatccc caaaaggttg ggaacgcgtt cgagagctgc tgaaggatag
     1501 ccaaggcata tcagcactga agctgtactc atttttag
//
