LOCUS       CP054334                1512 bp    DNA     circular BCT 10-JUN-2020
DEFINITION  Escherichia coli strain SCU-121 plasmid pSCU-121-6, complete
            sequence.
ACCESSION   CP054334
VERSION     CP054334.1
DBLINK      BioProject: PRJNA624897
            BioSample: SAMN14609781
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 1512)
  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  JOURNAL   Unpublished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 1512)
  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                   :: 12x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 05/26/2020 18:38:34
            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)                     :: 4,901
            CDSs (total)                      :: 4,791
            Genes (coding)                    :: 3,570
            CDSs (with protein)               :: 3,570
            Genes (RNA)                       :: 110
            rRNAs                             :: 7, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 5
            Pseudo Genes (total)              :: 1,221
            CDSs (without protein)            :: 1,221
            Pseudo Genes (ambiguous residues) :: 0 of 1,221
            Pseudo Genes (frameshifted)       :: 1,095 of 1,221
            Pseudo Genes (incomplete)         :: 102 of 1,221
            Pseudo Genes (internal stop)      :: 95 of 1,221
            Pseudo Genes (multiple problems)  :: 67 of 1,221
            ##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..1512
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-121"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-121-6"
                     /geo_loc_name="USA: California"
                     /collection_date="2016"
     gene            complement(166..417)
                     /locus_tag="HHJ34_24500"
                     /pseudo=""
     CDS             complement(166..417)
                     /locus_tag="HHJ34_24500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001482226.1"
                     /note="incomplete; partial on complete genome; missing
                     C-terminus; Derived by automated computational analysis
                     using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="rep protein"
                     /name="rep protein"
     gene            1064..1504
                     /locus_tag="HHJ34_24505"
     CDS             1064..1504
                     /locus_tag="HHJ34_24505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000031238.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QKN43422.1"
                     /translation="MSKDVERITQINDQGEIIGGFVAVIRPKQKSAFQRHFTMNQDALR
                     ILAKELTGEQFKVLMLMLADLDYENFIQIAQADIAETLGMQKTNVSRAVRALLDVGVIF
                     EGPKVGRSKTYRLNEQFGWKGTVTNHKKALKNGFSVIQGGRI"
                     /name="hypothetical protein"
     Typing          complement(283..539)
                     /name="Col(MG828)"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.186"
                     /coverage="98.0"
                     /evalue="3.06e-107"
ORIGIN
        1 cggcaggcgg acaatcaggg ctacgtgtta acgttttgac catgattgtc tatcctgcat
       61 tgcattgctc ttttgccgca tgtcagttcg atgcgatgca ggatagggca aacgccgcaa
      121 aatgacgtca ttgacgtcat tcgcaacctt tgcccgataa tctccaaaac gtctgagctg
      181 ccacggttcc ggcagcgcct tgagcgcaac cggaaaccgt ctggggagaa ccccagaccc
      241 ccatcgctgt aacatcgacg gtctacgacc accaaccagc tgaatagctg ccagtgccgt
      301 gcaaatgggc tttgcagggg gctgacgcgg ttcctggcga cctgaaagcc cctggttagg
      361 ggtatcggcg cgcctgacct cctgaaaccc tctgtaagcg tttttcgcgc cttccatgcc
      421 ctgacgggca tttaaaaccc gtttcgtgcg cctgagagct tctgagagcg tttgaagagc
      481 tatctggcga ctcatccccg aaagaacaac agcggaatca ccgataacat gcgagaggtg
      541 gcaccgctcg ccgcagcccc agcgaccgaa cgttagtgag cgagtgggcg aggaagcgga
      601 agagaaccgg aaaccacatt gagcacgtac gcactgatgc ggggtgtcgg ggtgaagccc
      661 tgaccagatg gcaaacggaa tatcgtcgcg ggtgacggta ttacatttgc acatcctgtc
      721 ccgatttctg cggagtttaa cggtgaacgg acggcaaaaa acgtgcagga gctgttgaac
      781 gtgaaaacct cgaaatctgg caaaaatcac ggctgacgag gcttgcagag gagtaagcca
      841 gtatacacat cgctatcgct ctgtgaactg ggtcagggct tcgccccgac accccaaaga
      901 gtagctagga taaatatcta atggaatcaa tgcgttagac gcctaatata aagatacaga
      961 aaggagaata aaaacattaa caaaatctaa gggttacagt tgacatagtt atcaataatg
     1021 ataacactgt tatcattatt gataactcaa atagggttca aagatgagta aggatgtcga
     1081 gagaatcact cagataaatg accagggtga gattatcggc ggcttcgttg ccgttatccg
     1141 ccctaaacaa aaatcagcat ttcagaggca tttcaccatg aatcaagacg cattacggat
     1201 cttggctaag gaattaaccg gggagcaatt caaggtctta atgctgatgc ttgcagatct
     1261 ggattacgaa aacttcattc agatcgccca agcagatatt gctgaaactt tagggatgca
     1321 gaaaacgaat gttagtcgcg ccgttcgcgc gctactggat gttggggtga tctttgaggg
     1381 acctaaagtt ggcagatcaa aaacataccg gctgaatgaa caatttggtt ggaaaggcac
     1441 cgtaaccaac cacaaaaagg cactcaaaaa cggctttagt gtcattcagg gcggccggat
     1501 ttaaagagcc ag
//
