LOCUS       CP054452                5064 bp    DNA     circular BCT 14-JUN-2020
DEFINITION  Escherichia coli strain SCU-488 plasmid pSCU-488-3, complete
            sequence.
ACCESSION   CP054452
VERSION     CP054452.1
DBLINK      BioProject: PRJNA624897
            BioSample: SAMN14943542
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5064)
  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  JOURNAL   Unpublished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 5064)
  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 v. 2.6
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 44x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/04/2020 19:12:22
            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)                     :: 5,111
            CDSs (total)                      :: 4,995
            Genes (coding)                    :: 3,821
            CDSs (with protein)               :: 3,821
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 1,174
            CDSs (without protein)            :: 1,174
            Pseudo Genes (ambiguous residues) :: 0 of 1,174
            Pseudo Genes (frameshifted)       :: 1,057 of 1,174
            Pseudo Genes (incomplete)         :: 111 of 1,174
            Pseudo Genes (internal stop)      :: 69 of 1,174
            Pseudo Genes (multiple problems)  :: 60 of 1,174
            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..5064
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-488"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-488-3"
                     /geo_loc_name="USA: California"
                     /collection_date="2018"
     gene            join(4915..5064,1..665)
                     /locus_tag="HPE47_25525"
                     /pseudo=""
     CDS             join(4915..5064,1..665)
                     /locus_tag="HPE47_25525"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001738986.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            complement(869..1267)
                     /locus_tag="HPE47_25530"
     CDS             complement(869..1267)
                     /locus_tag="HPE47_25530"
                     /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="QKP94439.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLIDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKELKYDLETSPNPDA"
                     /name="hypothetical protein"
     gene            1444..2370
                     /locus_tag="HPE47_25535"
     CDS             1444..2370
                     /locus_tag="HPE47_25535"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobA/MobL family protein"
                     /protein_id="QKP94440.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTAPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            2373..2906
                     /locus_tag="HPE47_25540"
     CDS             2373..2906
                     /locus_tag="HPE47_25540"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QKP94441.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISQDFQRLEESVANMKANADALSRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTILDRNYNATAAVYQKVVTLED
                     KLVEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            complement(2972..3181)
                     /locus_tag="HPE47_25545"
     CDS             complement(2972..3181)
                     /locus_tag="HPE47_25545"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_019842149.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QKP94442.1"
                     /translation="MAKLGENTPHIIDATVDFMASSQAFREYLKKLPPDNTIPPALTDE
                     HVPLYIRRLEYYRLLYRPKQTESY"
                     /name="hypothetical protein"
     Typing          2..511
                     /name="rep_cluster_2131"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.804"
                     /coverage="90.0"
                     /evalue="0.0"
     Typing          1445..2367
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctcacctgct ctacgcactc aacatcgccg tgagaaccgc gcctgatgcc tcggttaagg
       61 cgctgaaata tgccgcagcg gttgaacgtt cgctgtgtga gaaactttgt gcggatgtga
      121 actacagcgg cctgatttgc aaaaatccgt tccacctgga atggctggtg atggagtggc
      181 gcgaggaagc ctataccctc gatgaactgg ctgattatct cgatttgagc gcctcagagc
      241 gtcgtagcat cgataaacat tacgggatgg ggcgaaactg ccacctgttc gaaatgacgc
      301 gcaaatgggc ttacagggcg attcgtcagg gctggccagc gttctcacag tggcttgaag
      361 cggtgatcca gcgtgtcgaa atgtacaatg catcgcttcc cgttccgctt tcactggctg
      421 aatgtcgggc tattggcaag agcattgcga aatacacgca caggaacttc acgccggaaa
      481 ctttcgcaca gtatgtggct gatacgcaca cgccagaaat tcaggctgca cgcggtcgca
      541 agggcggttc taagtctaag cgcagcacag tagctacatc tgcacgcacg ctgaaaccgt
      601 gggaggcatt agggatcagt cgcgcctggt attaccaact gaaaaaacga ggtctcgtag
      661 agtagaccaa ataagcctat atcagataac agcgcctttc tggcgtcttt ttgagcagca
      721 ggttttttgc cgtttttccc cgttcagccc tgcaatggcg cggctttccg cgtgattgtg
      781 gtggtagtgc tcgccgcagt ctcatgaccg agcgtagcga gcgaatgagc gaggaagcac
      841 cagggaatcg gaacacggat ggaggcactt acgcgtctgg gtttggggat gtctccagat
      901 cgtacttaag ttccttaagt gcttgtaata tcctgtcttt tttatagcat agctcgcctg
      961 tttttgtgtc taccagtcct gcttcgatca gtagcccagc cgcgagaaag agccggtgat
     1021 tgcgttcccg tcgttgtttt tttccctcga ttcgtttttg gaccgcctgt tttcgttcgc
     1081 tctcctgtgc ctgtaagtcg tttttttccg ctgttgccag tacgtggaga agtttgcgtt
     1141 cctgttctgt gagtccggct tcgttgtcga tcaggtcaat aatctgtctc tgtcgtgcgg
     1201 tctgttctcc gagcttcctg atgaatccga tccgtttctt cagccattcg atgttgctga
     1261 tgcgcatgtt cgtgatgctc ctggtgtttt tttgcggtgt gttgtggtcg tgcagtatat
     1321 cgcttgcggt cggcgggtgc agggggtatc ttccgtgcta attcgtaaaa ttagaaggaa
     1381 gcgcacttat atgtttctct ccttcgtcga gaaaacagtg cgctcctgca gagggctgaa
     1441 accgtggcaa cctatcacct cagcgttaaa tttggtggca aggggcaggc tgcaaaccac
     1501 gccgattaca tcgagcgcaa agagaaatac cgcgaccgtc aggatttgga atattccgca
     1561 cacggaaaca tgccggaatg ggccagggat aatccttccc atttctggca ggcggctgac
     1621 cagtttgaac gtgcgaacgg ttcgacctat agggaacttg aaattgcatt accccgtgaa
     1681 ctgacaccgg aacagcgcct tgaactggtg caggattttg tacgtcagga agctggcgaa
     1741 cggcacgcct ggagttttgc cattcacaat ccgaaagcga gcattgacgg cggcgaacag
     1801 cctcatgcgc atatcatgat gagtcagcgt gtgaatgatg gcattgaacg tacaccggaa
     1861 cagtatttcc ggcgctataa cgccaggtat cccgagcggg gaggtgcgaa aaaggattcc
     1921 ggaagcctga ctctcactca gcaaaaagag cagttgcggg aattgcgaaa acgctgggag
     1981 gtgaagcaca acgaacatat gagaaagcat ggctttgaaa ggggcttcat tgactgccgg
     2041 acgctgaaag aacagggcat tgaacgacgt cccgaagtgc atctgggttt tgaagctgcc
     2101 ggacggcttg atgatgccca gcgtcatgac atcatgcaaa aacggtctga accggactat
     2161 tcccgccatc ttgaacaggc gcgaacggtc gggcatgaca tcagggaatg gctggacact
     2221 ccggttaagc aacatgaact ggtcagaagg ctgcaacatg atgttgcgcg ggagcatggc
     2281 tttgacatga gagacagagt gagcagacag aaccgaactg cacctgaacg ggttaaatca
     2341 ccgtcacgtg gattttctat gggattctga acatggccag cacagaagaa aaattactca
     2401 cgctcctgtt atcggtggag catctgcaac ataccgcaat ggagcaacag aaagctgttg
     2461 ctgattctct ggctgtggca agggaaactc ttcgcggata tcgggatatt tctgacggtg
     2521 tggcaaaaca ggtcagggat gaagtcagaa atgaggtgca gaagctggac gtggcaggac
     2581 tgataggtga gcgcatcagc caggattttc agcggctgga agagtcagtc gcaaacatga
     2641 aggcaaacgc ggatgccctg agcagggata ttgcgacaat tcacagcaat atcgtgcagg
     2701 aatacaacac ccttaaaggg tatagctgga aatggctggg tggggtgtca gtggcttttc
     2761 tggttatgtt ctgtgtgctc ggatggggaa tgaaaacaat actcgacagg aactacaacg
     2821 ccacagcggc ggtgtatcag aaagttgtga cactggaaga taaactggtg gagaaacctg
     2881 tcacggggaa gagccggaaa aactgacgcg cttcgcttgt ccaacgcctc acgacccgcg
     2941 aaaggatttc gcgaaccgtt caccgttttt ttcaatatga ttctgtctgc tttggtcgat
     3001 aaagcagacg atagtattcc agccttcgta tatataacgg tacgtgctca tcagtaagag
     3061 ctggcggtat tgtgttatca gggggaagtt ttttcagata ctcacgaaat gcctggcttg
     3121 atgccataaa atctacagta gcatcgataa tatgtggggt gttttcacct aattttgcca
     3181 tgatgataat ccttatatta tcacggtttg tgaatgatag gggtgtcact attatttatg
     3241 cgttagtgaa ccagaaaaaa tcccccgttg gcataggggg atatgtaagg agaaataact
     3301 tcgcaggtgt tcttgtttgt ataacgtgaa aagactgcac gcaacttaat aagtctgccg
     3361 tacttacttt cagttttcaa cataaggttt ataacaatgt atggaatgga agtgagcttt
     3421 aaggtttcag ctctaaaaaa taaaatattt attagttggc tggttgttgt tcttgttctg
     3481 tatgtatata aacactatcg acatattatg accgagaaca ttccttaccc cctctgcgct
     3541 cgcagaggtt ttttttgtca ttaattaata atgaactgaa atgcagttcc gatacctcca
     3601 tttgcacatt atccctgaca tatggtaccg gaaccgcatt aattttatgt tataagagtt
     3661 tatttttaat gtccagatgg tttaatagta tttatatgta attagctgta tggatagtac
     3721 tggttttatt gtataacttg tcgttttttt tattgttttt gtgtggtgtg ctaatcttta
     3781 agttataaaa aaccccttgg aatacagggg caaaagtaag gaaaacaaat ggatgctcag
     3841 tttgtgtgac actttaaact aatggaacta tagagtggag gttgttacag tcgcttttat
     3901 aaaacagcaa ccagtttttt tcaatagtct gatgatggtt gtgacagttt tgtgatattg
     3961 ttcaaaatgt ttcttgttga atgtttgttt tttggtctat tggtgtctgg ttttattttt
     4021 tctgctatta catatcaaga aatgtgattg gtgtagcaag agtggaatgc gatgtggata
     4081 aactaattgg ttgtcgaatc taatttactt agaaaactac acttgttttt gtgtatgaat
     4141 ttagtgaatt tgtctgtcta tgtgttttcg tgcatttata aatccttcgt caggatctta
     4201 aatttagtgt tgaatatgta gggcctgtac ggtaattatt atttagcgta gctacttcat
     4261 cgttgttcga acacaaccaa caacctgtaa ttgttgtttc tcttggttcc ccacttttgt
     4321 ggggtttttt atctcttccg tgcatcgtaa agcgcggact ccttctggaa aggttgtttt
     4381 agggcatcac tgaggcattt tttgcgtttg tgaatattga gcatccgata actaaaatat
     4441 ttcccataga ctctgattct tgccaccgac cccaggtcgg tttttttttg tcctggcgag
     4501 atgtgaagtt tggaaacagg aaaccccgtc agagcgccac gcaccagggg agaaaacttg
     4561 tcgttttgag ccgttcggtg ttcagaacgc acgaaaccga tcgcacatcg ctttcgtgca
     4621 tagttatgca acgccctgaa aacgattctg acgcgttttt ctggtttggc ctggtgtttt
     4681 cttgtctttt tgcgtttttt gcgccagaaa gcgattgagg gcgttttaca tggtacgtac
     4741 aacgggagtt atggtaaatg gatcggattt gcgggaaggc tcgacaggtt ttgtcgttgg
     4801 gggtagtgta agcgactgaa aaacaaacgc ccctgaaatt cgtgtctatc cgccaagact
     4861 ttcacgaaaa tacaggggcg atgtcggtcg ataacctgga aggaatcgta acacatgagc
     4921 gccgcgcttc aatacttcga agaaaattta ccccaccgtc cctatcacac ggatgatctc
     4981 gctttcggcc ttcgtatctc cggcaaaggg cgcgcgcttc ttgcacggta tatccagcag
     5041 aaccagcctc atgcacagtt ctgg
//
