LOCUS       CP054464                1546 bp    DNA     circular BCT 14-JUN-2020
DEFINITION  Escherichia coli strain SCU-103 plasmid pSCU-103-7, complete
            sequence.
ACCESSION   CP054464
VERSION     CP054464.1
DBLINK      BioProject: PRJNA624897
            BioSample: SAMN14943534
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1546)
  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  JOURNAL   Unpublished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 1546)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Hartman,A., Gonzalez,A.,
            Gill,M., Pandori,M. and Hess,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-JUN-2020) Biology, Santa Clara University, 500 El
            Camino Real, Santa Clara, CA 95054, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye, Unicycler v. 2.6, 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 57x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/04/2020 20:11:23
            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)                     :: 5,482
            CDSs (total)                      :: 5,353
            Genes (coding)                    :: 3,705
            CDSs (with protein)               :: 3,705
            Genes (RNA)                       :: 129
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 92
            ncRNAs                            :: 15
            Pseudo Genes (total)              :: 1,648
            CDSs (without protein)            :: 1,648
            Pseudo Genes (ambiguous residues) :: 0 of 1,648
            Pseudo Genes (frameshifted)       :: 1,488 of 1,648
            Pseudo Genes (incomplete)         :: 174 of 1,648
            Pseudo Genes (internal stop)      :: 59 of 1,648
            Pseudo Genes (multiple problems)  :: 68 of 1,648
            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/
            NCBI analysis of this genome has determined that >30% of the
            predicted CDS features contain frameshifts, which is well above the
            usually observed value of <10%.
FEATURES             Location/Qualifiers
     source          1..1546
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-103"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-103-7"
                     /geo_loc_name="USA: California"
                     /collection_date="2015"
     gene            1..477
                     /locus_tag="HPE39_27405"
     CDS             1..477
                     /locus_tag="HPE39_27405"
                     /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="QKQ01922.1"
                     /translation="MFIDSEKRLKQLSDEAKKNTEDLEEAKKNSRFTQVSPKGWERVRE
                     LLKDSQGISALKLYSFLAEHIDPTCGAVVADQQFLAEKLGVSRSTIIRWLNYLESKNAL
                     VRIPVAGKVCAYALDPHEVWKGYNTTKNYAAFVTKTLVNKDGDIQRRIMAMFSN"
                     /name="helix-turn-helix domain-containing protein"
     gene            896..1048
                     /locus_tag="HPE39_27410"
     CDS             896..1048
                     /locus_tag="HPE39_27410"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QKQ01923.1"
                     /translation="MFEGLSDDSSPKEQQRDHRQHARGDPARRKSMTERSERIDEEAEE
                     NRKLH"
                     /name="hypothetical protein"
     Typing          1082..1163
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          complement(1360..1468)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.95e-50"
     Typing          complement(710..967)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.0"
                     /coverage="99.0"
                     /evalue="3.93e-111"
ORIGIN
        1 atgtttattg attcagaaaa acgactgaaa caactttcag atgaggcaaa gaaaaacacc
       61 gaggatctcg aagaagcaaa gaagaattca aggtttacac aggtatcccc aaaaggttgg
      121 gaacgcgttc gagagctgct gaaggatagc caaggcatat cagcactgaa gctgtactca
      181 tttttagcgg agcatatcga tcctacgtgt ggcgctgtcg ttgcggatca gcaattccta
      241 gctgaaaaac ttggagttag cagaagcaca attattcggt ggctcaatta cttagaatca
      301 aaaaatgcat tagttagaat ccccgttgct ggtaaggttt gtgcgtatgc cctcgatcca
      361 catgaagtct ggaagggata caacactacg aaaaactatg cagcgtttgt cactaaaaca
      421 ctggtcaaca aagacggtga tattcagcgc cgaatcatgg ccatgttttc aaattgagcc
      481 agcggcaggc ggacaatcag gggctacgtg ttaacgtttt gaccatgatt gtctatcctg
      541 cattgctctt ttgccgcctc aaaatccctt gcgtgttttt gctccccgat ccccagaacg
      601 accgcgccgc cacggttccg gcagcgcctt gagcgcaacc ggaaaccgtc tggggagaac
      661 cccagacccc catcgctgta acaccgacgg tctacgacca ccaaccagcc gaatagctgc
      721 ctgtgccgtg caaataggct ttgcagggag ctgacgcggt tcctagcgac ctgaaagccc
      781 ctggttaggg gtatcggcgc gcctgacctc ctgagagcct ctgtaagcgt ttttcgcgcc
      841 ttccatgccc tggcgggcat ttaaacccgt ttcgtgcgtc tgaaagcttc tgagcgtgtt
      901 tgaagggcta tctgacgact catccccgaa agaacaacaa cgggatcacc gacaacatgc
      961 gagaggtgat cccgctcgcc gcaagtcgat gaccgagcgt agcgagcgaa tcgacgagga
     1021 agcggaagag aaccggaagt tacattgagc acttacgcac ggatgcgggg tgtcggggtg
     1081 aagccctgac caggtgggga atgtctgagt gcgcgtgcgc ggtccgacat tcccacatcc
     1141 tgtcccgatt tctgaggcgt tttaacggtg aacggacggc aaaaacatga tcgagctgtt
     1201 gaacgtggag agcgcgaaat cgggcaaaat cacggctgac gaggcttgca gaggagtaag
     1261 ccagtataca ctccgctatc gctacgtgac tgggtcaggg cttcgccccg acaccccaaa
     1321 agggcgttgc gttgcgcgca acacccttgc ctagaataga tcttttacgc cgatttgtaa
     1381 gttgttgttt ttttagtgtg ttttttgttt acctgtcgca tccagggtga cacaacgttg
     1441 tcgcatccag gatgcgacaa cacgcaacaa ggtgttgcac agatgtgtca tgatggctta
     1501 gatttgaacc aacgttagtg catgggattt tcagagggaa aaaatc
//
