LOCUS       NZ_CP054362             1552 bp    DNA     circular CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-172 plasmid pSCU-172-9, complete
            sequence.
ACCESSION   NZ_CP054362
VERSION     NZ_CP054362.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14943545
            Assembly: GCF_013315695.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1552)
  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  JOURNAL   Unpublished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 1552)
  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                   :: 78x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 03:55:40
            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)                     :: 5,461
            CDSs (total)                      :: 5,339
            Genes (coding)                    :: 5,056
            CDSs (with protein)               :: 5,056
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 94
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 283
            CDSs (without protein)            :: 283
            Pseudo Genes (ambiguous residues) :: 0 of 283
            Pseudo Genes (frameshifted)       :: 85 of 283
            Pseudo Genes (incomplete)         :: 198 of 283
            Pseudo Genes (internal stop)      :: 39 of 283
            Pseudo Genes (multiple problems)  :: 33 of 283
            Pseudo Genes (short protein)      :: 3 of 283
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054362.1.
            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..1552
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-172"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-172-9"
                     /geo_loc_name="USA: California"
                     /collection_date="2017"
     gene            136..612
                     /locus_tag="HPE50_RS26965"
                     /old_locus_tag="HPE50_26975"
     CDS             136..612
                     /locus_tag="HPE50_RS26965"
                     /old_locus_tag="HPE50_26975"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000469298.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_000469298.1"
                     /translation="MFIDSEKRLKQLSDEAKKNTEDLEEAKKNSRFTQVSPKGWERVRE
                     LLKDSQGISALKLYSFLAEHIDPTCGAVVADQQFLAEKLGVSRSTIIRWLNYLESKNAL
                     VRIPVAGKVCAYALDPHEVWKGYNTTKNHAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     Typing          1206..1291
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="91.954"
                     /coverage="95.0"
                     /evalue="4.39e-26"
     Typing          complement(843..1103)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="93.511"
                     /coverage="100.0"
                     /evalue="3.95e-106"
ORIGIN
        1 cctgtcgcat ccagggtgac acaacgttgt cgcatcctgg atgcgacaac acgcaacaag
       61 gtgttgcaca gatgtgtcat gatggcttag atttgaacca acgttagtgc atgggatttt
      121 tagagggaaa aaatcatgtt tattgattca gaaaaacgac tgaaacaact ttcagatgag
      181 gcaaagaaaa acaccgagga tctcgaagaa gcaaagaaga attcaaggtt tacacaggta
      241 tccccaaaag gttgggaacg cgttcgagag ctgctgaagg atagccaagg catatcagca
      301 ctgaagctgt actcattttt agcggagcat atcgatccta cgtgtggcgc tgtcgttgcg
      361 gatcagcaat tcctagctga aaaacttgga gttagcagaa gcacaattat tcgttggctc
      421 aattacttag aatcaaaaaa tgcattagtt agaatccccg ttgctggtaa ggtttgtgcg
      481 tatgccctcg atccacatga agtctggaag ggatacaaca ctacgaaaaa ccatgcagca
      541 tttgtcacta aaacactggt caacaaagac ggtgatattc agcgccgaat catggccatg
      601 ttttcaaatt gagccagcgg caggcggaca atcaggggct acgtgttaac gttctgacca
      661 tgattgtcta tcctgcattg ctcttttgcc gcctcaaaat cccttgcgtg tttttgctcc
      721 ccgatctcca gaacgaccga gccgccacgg ttccggcagc gccttgagcg caaccggaaa
      781 ccgtctgggg agaaccccag acccccatcg ctgtaacacc gacggtctac gaccacctac
      841 caaccgagtg actgcctgta ccgtgcaaat gggctttgca gggggctggc gcggttcctg
      901 gcgacctgaa agcccctggc taggggtatc ggcgcgcctg acctcctgaa acgctctgta
      961 agcgtttttc gcgccttcca tgccctgacg ggcatttaaa ccccgcctcg tgcgtctgag
     1021 agcttctgag cgcgtttgaa gggctatctg acgactcatc cccgaaagaa caacagcgga
     1081 atcaccgaca acatgcgaga ggtggcaccg ctcgccgcag ccccagcgac cgaacgttag
     1141 tgagcgagtg ggcgaggaag cggaagagaa ccggaaacca cattgagcac gtacgcactg
     1201 atacggggtg tcggggcgaa gccctgacca gatggcaaac ggaatatcgt cgcgggtgac
     1261 ggtattacat ttgcacatcc tgtcccgatt tctgcggggg ttaacggtga acggacggca
     1321 aaaaacgtgc aggagctgtt gaacgtgaaa accacgaaat ctggcaaaaa tcacggctgg
     1381 cgaggcttgc agaggagtaa gccagtatac actccgctat cgctacgtga ctgggtcagg
     1441 gcttcgcccc gacaccccca aagggcgttg cgttgcgcgc aacacccttg cctagaatag
     1501 atcttttacg ccgatttgta agttgttgtt tttttagtgt gttttttgtt ta
//
