LOCUS       CP054463                2100 bp    DNA     circular BCT 14-JUN-2020
DEFINITION  Escherichia coli strain SCU-103 plasmid pSCU-103-6, complete
            sequence.
ACCESSION   CP054463
VERSION     CP054463.1
DBLINK      BioProject: PRJNA624897
            BioSample: SAMN14943534
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 2100)
  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  JOURNAL   Unpublished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 2100)
  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..2100
                     /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-103-6"
                     /geo_loc_name="USA: California"
                     /collection_date="2015"
     gene            complement(join(1155..2100,1..20))
                     /locus_tag="HPE39_27395"
     CDS             complement(join(1155..2100,1..20))
                     /locus_tag="HPE39_27395"
                     /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="QKQ01921.1"
                     /translation="MSEDKFLSDYSPRDAVWDTQRTLTDSVGGIYQTAAEFERYALRMA
                     SCSGLLRFGWSTIMETGETRLRLRSAQFCRVRHCPVCQWRRTLMWQARFYQALPKIVVD
                     YPSSRWLFLTLTVRNCEIGELGTVLTAMNAAFKRMEKRKELSPVQGWIRATEVTRGKDG
                     SAHPHFHCLLMVQPSWFKGKNYVKHERWVELWRDCLRVNYEPNIDIRAVKTKTGEVVAN
                     VAEQLQSAVAETLKYSVKPEDMANDPEWFLELTRQLHKRRFISTGGALKNVLQLDRETN
                     EDLVIADDVGDGTDDGKRTAFVWDSGKRRYKRAPEKDKSD"
                     /name="protein rep"
     gene            complement(885..1151)
                     /locus_tag="HPE39_27400"
     CDS             complement(885..1151)
                     /locus_tag="HPE39_27400"
                     /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="QKQ01920.1"
                     /translation="MNINIEYLNGNKTIGLFFLRSEAVIPDRFKNLILLIDGLSFGTFG
                     FHPHEGFEDELILYIQKTNERVKTLFVKIDLNGIKFGFLRTHS"
                     /name="hypothetical protein"
     Typing          complement(1496..1727)
                     /name="Col(BS512)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="2.05e-118"
ORIGIN
        1 aggaatttat cttctgacat taagcctgct ccgatctggg caggctgtga tttgatgtgg
       61 tatattcatc acgtacctgt gcattgcgag ccagtacatg tcaccagagt ttgccgctga
      121 ggtgacacat tcgaaatgtt ggggagtgtt gacgcactcc ccaacgccga ttaaaaacgc
      181 ctcaattctg ctccattttc tttgacctgt caaaacccac tcaaagcctc gtcattactg
      241 ggctaaacca ctatttcata tccgccattt atcccttaag tataaataca aggatcacgc
      301 gcgagaattg cgcaaaaaat aaccacaatt ttaaccccca aaacaagcac ccccgaacgg
      361 cttaccccaa ccttttccac acacccgatc accaaaacag ggaataaaaa caaaaccctg
      421 tcttacaggt ggatggcctc acttcgtgaa accatccacc ccgcataagt tttttaatcg
      481 gtggtgtcgt caatcactaa atcggaaccc caaaggggac ccccacgatt tagcatttga
      541 cgagattaac tctcggagat ggcatcatgc ttttaacgga ctttaaaaaa cggtgaacgg
      601 atgcggattt taatccgtgt ctgtgaggcg ttgagcaacg agcaaagcga ggcggtagaa
      661 agagagccag cggcaggctc aggacgataa tccggggaaa atgtaccact cgcagagtgt
      721 taacatttga catcggattg tctatcctgc attggtgtcg agttggcaag gctgaggata
      781 atgctgagga taatgctgag gataatgcag gatagacaga gcactagaga ttgcatgcaa
      841 tctcgtacct atcacctcag cctgccgctg gctcttttcc agaactaaga atgcgttctt
      901 aaaaatccaa acttgatacc gtttaaatct attttcacaa aaagagtttt taccctctcg
      961 tttgttttct gaatatataa aattaattca tcctcaaaac cttcgtgcgg atgaaaacca
     1021 aatgtgccaa aacttaatcc atcaataagc aaaataaggt ttttaaacct gtcaggaatc
     1081 accgcttcac ttcttaaaaa aaataaacca atagtcttat ttccattcag gtattcaata
     1141 ttaatattca tacgttaatc cgatttatcc ttctcagggg cgcgtttgta acgccgttta
     1201 cctgaatccc agacaaacgc cgtccgcttc ccgtcatcag tgccatcccc tacatcgtcg
     1261 gcaatgacaa gatcctcatt ggtttctcga tccaactgga ggacgttttt tagcgcccca
     1321 ccggtcgaga taaaacggcg cttgtgaagc tgccgcgtca gctcaagaaa ccactcagga
     1381 tcgtttgcca tatcttccgg tttaacggag tatttcagcg tttcagcaac cgcgctttgc
     1441 agttgctcgg caacgttggc cacaacctca cctgtcttag tttttactgc ccgaatatcg
     1501 atattcggct catagttcac ccgcaagcaa tcgcgccaga gttctaccca acgttcgtgc
     1561 ttaacgtagt tcttcccttt aaaccaagaa ggttgcacca tcagcagaca gtgaaaatgc
     1621 ggatgtgcgc tgccatcctt acctcgcgtc acctccgtag ccctgatcca cccctgaaca
     1681 ggtgatagct cctttcgctt ttccattcgc ttaaacgccg cattcattgc tgtaaggact
     1741 gttccaagtt cacctatctc gcagttcctg acagttaacg tcagaaacaa ccatcgggaa
     1801 gacgggtaat ccacaacgat tttcggtaga gcctgataaa aacgggcttg ccacatgagg
     1861 gttcttctcc actggcagac agggcaatga cggacacggc aaaattgcgc actacgaagc
     1921 cgtaggcgcg tttctccggt ttccatgatg gtagaccaac caaaacgtaa caaaccgcta
     1981 caggaggcca tacggagtgc atagcgctcg aattcagcag cagtctggta gatacccccg
     2041 acagaatcgg taagcgtgcg ctgggtatcc caaactgcat cacgggggct gtagtccgaa
//
