LOCUS       CP054341                2088 bp    DNA     circular BCT 10-JUN-2020
DEFINITION  Escherichia coli strain SCU-120 plasmid pSCU-120-6, complete
            sequence.
ACCESSION   CP054341
VERSION     CP054341.1
DBLINK      BioProject: PRJNA624897
            BioSample: SAMN14609780
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2088)
  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  JOURNAL   Unpublished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 2088)
  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..2088
                     /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-120-6"
                     /geo_loc_name="USA: California"
                     /collection_date="2016"
     gene            join(1200..2088,1..77)
                     /locus_tag="HHJ33_26605"
     CDS             join(1200..2088,1..77)
                     /locus_tag="HHJ33_26605"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012421200.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="protein rep"
                     /protein_id="QKN47632.1"
                     /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQTAAEFERYALRMA
                     SCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIVVD
                     YPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRGKDG
                     SAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGEVVAN
                     VAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQLDRETN
                     EDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD"
                     /name="protein rep"
     gene            81..347
                     /locus_tag="HHJ33_26610"
     CDS             81..347
                     /locus_tag="HHJ33_26610"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001024536.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QKN47631.1"
                     /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTFG
                     FHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS"
                     /name="hypothetical protein"
     Typing          1594..1825
                     /name="Col(BS512)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.05e-118"
ORIGIN
        1 ggaagcggac ggcgtttgtc tgggattcag gtaaacggcg ttacaaacgc gcccctgaga
       61 aggataaatc ggattaacgt atgaatatta atattgaata cctgaatgga aataagacta
      121 ttggtttatt ttttttaaga agtgaagcgg tgattcctga caggtttaaa aaccttattt
      181 tgcttattga tggattaagt tttggcacat ttggttttca tccgcacgaa ggttttgagg
      241 atgaattaat tttatatatt cagaaaacaa acgagagggt aaaaactctt tttgtgaaaa
      301 tagatttaaa cggtatcaag tttggatttt taagaacgca ttcttagttc tggaaaagag
      361 ccagcggcag gctgaggtga taggtacgag attgcatgca atctctagtg ctctgtctat
      421 cctgcattat cctcagcatt atcctcagcc ttgccaactc gacaccaatg caggatagac
      481 aatccgatgt caaatgttaa cactctgcga gtggtacatt ttccccggat tatcgtcctg
      541 agcctgccgc tggctctctt tctaccgcct cgctttgctc gttgctcaac gcctcacaga
      601 cacggattaa aatccgcatc cgttcaccgt tttttaaagt ccgttaaaag catgatgcca
      661 tctccgagag ttaatctcgt caaatgctaa atcgtggggg tcccctttgg ggttccgatt
      721 tagtgattga cgacaccacc gattaaaaaa cttatgcggg gtggatggtt tcacgaagtg
      781 aggccatcca cctgtaagac agggttttgt ttttattccc tgttttggtg atcgggtgtg
      841 tggaaaaggt tggggtaagc cgttcggggg tgcttgtttt gggggttaaa attgtggtta
      901 ttttttgcgc aattctcgcg cgtgatcctt gtatttatac ttaagggata aatggcggat
      961 atgaaatagt ggtttagccc agtaatgacg aggctttgag tgggttttga caggtcaaag
     1021 aaaatggagc agaattgagg cgtttttaat cggcgttggg gagtgcgtca acactcccca
     1081 acatttcgaa tgtgtcacct cagcggcaaa ctctggtgac atgtactggc tcgcaatgca
     1141 caggtacgtg atgaatatac cacatcaaat cacagcctgc ccagatcgga gcaggcttaa
     1201 tgtcagaaga taaattcctt tcggactaca gcccccgtga tgcagtttgg gatacccagc
     1261 gcacgcttac cgattctgtc gggggtatct accagactgc tgctgaattc gagcgctatg
     1321 cactccgtat ggcctcctgt agcggtttgt tacgttttgg ttggtctacc atcatggaaa
     1381 ccggagaaac gcgcctacgg cttcgtagtg cgcaattttg ccgtgtccgt cattgccctg
     1441 tctgccagtg gagaagaacc ctcatgtggc aagcccgttt ttatcaggct ctaccgaaaa
     1501 tcgttgtgga ttacccgtct tcccgatggt tgtttctgac gttaactgtc aggaactgcg
     1561 agataggtga acttggaaca gtccttacag caatgaatgc ggcgtttaag cgaatggaaa
     1621 agcgaaagga gctatcacct gttcaggggt ggatcagggc tacggaggtg acgcgaggta
     1681 aggatggcag cgcacatccg cattttcact gtctgctgat ggtgcaacct tcttggttta
     1741 aagggaagaa ctacgttaag cacgaacgtt gggtagaact ctggcgcgat tgcttgcggg
     1801 tgaactatga gccgaatatc gatattcggg cagtaaaaac taagacaggt gaggttgtgg
     1861 ccaacgttgc cgagcaactg caaagcgcgg ttgctgaaac gctgaaatac tccgttaaac
     1921 cggaagatat ggcaaacgat cctgagtggt ttcttgagct gacgcggcag cttcacaagc
     1981 gccgttttat ctcgaccggt ggggcgctaa aaaacgtcct ccagttggat cgagaaacca
     2041 atgaggatct tgtcattgcc gacgatgtag gggatggcac tgatgacg
//
