LOCUS       CP054342                1552 bp    DNA     circular BCT 10-JUN-2020
DEFINITION  Escherichia coli strain SCU-120 plasmid pSCU-120-7, complete
            sequence.
ACCESSION   CP054342
VERSION     CP054342.1
DBLINK      BioProject: PRJNA624897
            BioSample: SAMN14609780
KEYWORDS    .
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., Gonzalez,A., Gill,M.,
            Hartman,A., Pandori,M. and Hess,D.
  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  JOURNAL   Unpublished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., Gonzalez,A., Gill,M.,
            Hartman,A., Pandori,M. and Hess,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (20-MAY-2020) Biology, Santa Clara University, 500 El
            Camino Real, Santa Clara, CA 95054, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye v. 2.6
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 35x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 05/26/2020 18:46:26
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 4.11
            Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA; repeat_region
            Genes (total)                     :: 5,323
            CDSs (total)                      :: 5,202
            Genes (coding)                    :: 4,211
            CDSs (with protein)               :: 4,211
            Genes (RNA)                       :: 121
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 94
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 991
            CDSs (without protein)            :: 991
            Pseudo Genes (ambiguous residues) :: 0 of 991
            Pseudo Genes (frameshifted)       :: 886 of 991
            Pseudo Genes (incomplete)         :: 117 of 991
            Pseudo Genes (internal stop)      :: 48 of 991
            Pseudo Genes (multiple problems)  :: 54 of 991
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            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/
FEATURES             Location/Qualifiers
     source          1..1552
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-120"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-120-7"
                     /geo_loc_name="USA: California"
                     /collection_date="2016"
     gene            171..647
                     /locus_tag="HHJ33_26615"
     CDS             171..647
                     /locus_tag="HHJ33_26615"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000469298.1"
                     /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="QKN47633.1"
                     /translation="MFIDSEKRLKQLSDEAKKNTEDLEEAKKNSRFTQVSPKGWERVRE
                     LLKDSQGISALKLYSFLAEHIDPTCGAVVADQQFLAEKLGVSRSTIIRWLNYLESKNAL
                     VRIPVAGKVCAYALDPHEVWKGYNTTKNHAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     Typing          complement(2..92)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="84.0"
                     /evalue="1.98e-40"
     Typing          1241..1326
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="93.103"
                     /coverage="95.0"
                     /evalue="9.44e-28"
     Typing          complement(878..1138)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.603"
                     /coverage="100.0"
                     /evalue="8.62e-98"
ORIGIN
        1 gtaagttgtt gtttttttag tgtgtttttt gtttacctgt cgcatccagg gtgacacaac
       61 gttgtcgcat cctggatgcg acaacacgca acaaggtgtt gcacagatgt gtcatgatgg
      121 cttagatttg aaccaacgtt agtgcatggg atttttagag ggaaaaaatc atgtttattg
      181 attcagaaaa acgactgaaa caactttcag atgaggcaaa gaaaaacacc gaggatctcg
      241 aagaagcaaa gaagaattca aggtttacac aggtatcccc aaaaggttgg gaacgcgttc
      301 gagagctgct gaaggatagc caaggcatat cagcactgaa gctgtactca tttttagcgg
      361 agcatatcga tcctacgtgt ggcgctgtcg ttgcggatca gcaattccta gctgaaaaac
      421 ttggagttag cagaagcaca attattcgtt ggctcaatta cttagaatca aaaaatgcat
      481 tagttagaat ccccgttgct ggtaaggttt gtgcgtatgc cctcgatcca catgaagtct
      541 ggaagggata caacactacg aaaaaccatg cagcatttgt cactaaaaca ctggtcaaca
      601 aagacggtga tattcagcgc cgaatcatgg ccatgttttc aaattgagcc agcggcaggc
      661 ggacaatcag gggctacgtg ttaacgttct gaccatgatt gtctatcctg cattgctctt
      721 ttgccgcctc aaaatccctt gcgtgttttt gctccccgat ctccagaacg accgagccgc
      781 cacggttccg gcagcgcctt gagcgcaacc ggaaaccgtc tggggagaac cccagacccc
      841 catcgctgta acaccgacgg tctacgacca cctgccaacc gcgtggctgc ctgttccgtg
      901 caaatgggct ttgcagcggg ctgacgcggt tcctggcgac ctgaaagccc ttggttaggg
      961 gtatcggcgc gcctgacctc ctgagactct ctgtaagcgt ttttcgcgcc ttccatgccc
     1021 tgacgggcat ttaaaacccg tttcgtgcgt ctgagggctt ctgagcgcgt ttgaggggct
     1081 atctggcgac tcatccccga aagggcaaca gcagaatcac cgacaacatg cgagaggtgg
     1141 caccgctcgc cgcagcccca gcgaccgaac gttagtgagc gagtgggcga ggaagcggaa
     1201 gagaaccgga aaccacattg agcacgtacg cactgatacg gggtgtcggg gcgaagccct
     1261 gaccagatgg caaacgtaat atcgtcgcgg gtgacggtat tacatttgca catcctgtcc
     1321 cgatttctgc gggggttaac ggtgaacgga cggcaaaaaa cgtgcaggag ctgttgaacg
     1381 tgaaaaccac gaaatctggc aaaaatcacg gctggcgagg cttgcagagg agtaagccag
     1441 tatacactcc gctatcgcta cgtgactggg tcagggcttc gccccgacac ccccaaaggg
     1501 cgttgcgttg cgcgcaacac ccttgcctag aatagatctt ttacgccgat tt
//
