LOCUS       CP054339                5166 bp    DNA     circular BCT 10-JUN-2020
DEFINITION  Escherichia coli strain SCU-120 plasmid pSCU-120-4, complete
            sequence.
ACCESSION   CP054339
VERSION     CP054339.1
DBLINK      BioProject: PRJNA624897
            BioSample: SAMN14609780
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5166)
  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  JOURNAL   Unpublished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 5166)
  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..5166
                     /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-120-4"
                     /geo_loc_name="USA: California"
                     /collection_date="2016"
     gene            693..902
                     /locus_tag="HHJ33_26540"
     CDS             693..902
                     /locus_tag="HHJ33_26540"
                     /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="QKN47620.1"
                     /translation="MAKLGENTPHIIDATVDFMASSQAFREYLKKLPPDNTIPPALTDE
                     HVPLYIRRLEYYRLLYRPKQTESY"
                     /name="hypothetical protein"
     gene            complement(968..1501)
                     /locus_tag="HHJ33_26545"
     CDS             complement(968..1501)
                     /locus_tag="HHJ33_26545"
                     /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="QKN47621.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQKLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTILDRNYNATAAVYQKVVTLED
                     KLVEKPVTGKSRKN"
                     /name="hypothetical protein"
     gene            complement(1504..2430)
                     /locus_tag="HHJ33_26550"
     CDS             complement(1504..2430)
                     /locus_tag="HHJ33_26550"
                     /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="QKN47622.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIDGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     LTQQKEQLRELRKRWEVKHNEHMRKHGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIREWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQNRTAPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            2487..3005
                     /locus_tag="HHJ33_26555"
     CDS             2487..3005
                     /locus_tag="HHJ33_26555"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221101.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="QKN47623.1"
                     /translation="MRFLLILRISTEDTPCTRRPQAIYCTTTTHRKKTPGSITNMRISN
                     IEWLKKRIGFIRKLGEQTARQRQIIDLIDNEAGLTEQERKLLHVLATAEKNDLQAQESE
                     RKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTGELCYKKDRILQALKELKYD
                     LETSPNPDA"
                     /name="hypothetical protein"
     gene            complement(3209..4123)
                     /locus_tag="HHJ33_26560"
     CDS             complement(3209..4123)
                     /locus_tag="HHJ33_26560"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001738986.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid replication protein"
                     /protein_id="QKN47624.1"
                     /translation="MSAALQYFDENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWLVMEWREEAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGSKSKRSTVATSARTL
                     KPWEALGISRAWYYQLKKRGLVE"
                     /name="plasmid replication protein"
     Typing          complement(3349..4123)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.778"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(1508..2430)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ctatagttcc attagtttaa agtgtcacac aaactgagca tccatttgtt ttccttactt
       61 ttgcccctgt attccaaggg gtttttttat aacttaaaga ttagcacacc acacaaaaac
      121 aataaaaaaa acgacaagtt atacaataaa accagtacta tccatacagc taattacata
      181 taaatactat taaaccatct ggacattaaa aataaactct tataacataa aattaatgcg
      241 gttccggtac catatgtcag ggataatgtg caaatggagg tatcggaact gcatttcagt
      301 tcattattaa ttaatgacaa aaaaaacctc tgcgagcgca gagggggtaa ggaatgttcc
      361 cggtcataat atgtcgatag tgtttatata catacagaac aagaacaaca accagccaac
      421 taataaatat tttatttttt agagctgaaa ccttaaagct cacttccatt ccatacattg
      481 ttataaacct tatgttgaaa actgaaagta agtacggcag acttattaag ttgcgtgcag
      541 tcttttcacg ttatacaaac aagaacacct gcgaagttat ttctccttac atatccccct
      601 atgccaacgg gggatttttt ctggttcact aacgcataaa taatagtgac accctatcat
      661 tcacaaaccg tgataatata aggattatca tcatggcaaa attaggtgaa aacaccccac
      721 atattatcga tgctactgta gattttatgg catcaagcca ggcatttcgt gagtatctga
      781 aaaaacttcc ccctgataac acaataccgc cagctcttac tgatgagcac gtaccgttat
      841 atatacgaag gctggaatac tatcgtctgc tttatcgacc aaagcagaca gaatcatatt
      901 gaaaaaaacg gtgaacggtt cgcgaaatcc tttcgcgggt cgtgaggcgt tggacaagcg
      961 aagcgcgtca gtttttccgg ctcttccccg tgacaggttt ctccaccagt ttatcttcca
     1021 gtgtcacaac tttctgatac accgccgctg tggcgttgta gttcctgtcg agtattgttt
     1081 tcattcccca tccgagcaca cagaacataa ccagaaaagc cactgacacc ccacccagcc
     1141 atttccagct atacccttta agggtgttgt attcctgcac gatattgctg tgaattgtcg
     1201 caatatccct gttcagggca tccgcgtttg ccttcatgtt tgcgactgac tcttccagcc
     1261 gctgaaaatc ctggctgatg cgctcaccta tcagtcctgc cacgtccagc ttctgcacct
     1321 catttctgac ttcatccctg acctgttttg ccacaccgtc agaaatatcc cgatatccgc
     1381 gaagagtttc ccttgccaca gccagagaat cagcaacagc tttctgttgc tccattgcgg
     1441 tatgttgcag atgctccacc gataacagga gcgtgagtaa tttttcttct gtgctggcca
     1501 tgttcagaat cccatagaaa atccacgtga cggtgattta acccgttcag gtgcagttcg
     1561 gttctgtctg ctcactctgt ctctcatgtc aaagccatgc tcccgcgcaa catcatgttg
     1621 cagccttctg accagttcat gttgcttaac cggagtgtcc agccattccc tgatgtcatg
     1681 cccgaccgtt cgcgcctgtt caagatggcg ggaatagtcc ggttcagacc gtttttgcat
     1741 gatgtcatga cgctgggcat catcaagccg tccggcagct tcaaaaccca gatgcacttc
     1801 gggacgtcgt tcaatgccct gttctttcag cgtccggcag tcaatgaagc ccctttcaaa
     1861 gccatgcttt ctcatatgtt cgttgtgctt cacctcccag cgttttcgca attcccgcaa
     1921 ctgctctttt tgctgagtga gagtcaggct tccggaatcc tttttcgcac ctccccgctc
     1981 gggatacctg gcgttatagc gccggaaata ctgttccggt gtacgttcaa tgccatcatt
     2041 cacacgctga ctcatcatga tatgcgcatg aggctgttcg ccgccgtcaa tgctcgcttt
     2101 cggattgtga atggcaaaac tccaggcgtg ccgttcgcca gcttcctgac gtacaaaatc
     2161 ctgcaccagt tcaaggcgct gttccggtgt cagttcacgg ggtaatgcaa tttcaagttc
     2221 cctataggtc gaaccgttcg cacgttcaaa ctggtcagcc gcctgccaga aatgggaagg
     2281 attatccctg gcccattccg gcatgtttcc gtgtgcggaa tattccaaat cctgacggtc
     2341 gcggtatttc tctttgcgct cgatgtaatc ggcgtggttt gcagcctgcc ccttgccacc
     2401 aaatttaacg ctgaggtgat aggttgccac ggtttcagcc ctctgcagga gcgcactgtt
     2461 tctcgacgaa ggagagaaac atataagtgc gcttccttct aattttacga attagcacgg
     2521 aagatacccc ctgcacccgc cgaccgcaag cgatatactg cacgaccaca acacaccgca
     2581 aaaaaacacc agggagcatc acgaacatgc gcatcagcaa catcgaatgg ctgaagaaac
     2641 ggatcggatt catcaggaag ctcggagaac agaccgcacg acagagacag attattgacc
     2701 tgatcgacaa cgaagccgga ctcacagaac aggaacgcaa acttctccac gtactggcaa
     2761 cagcggaaaa aaacgactta caggcacagg agagcgaacg aaaacaggcg gtccaaaaac
     2821 gaatcgaggg aaaaaaacaa cgacgggaac gcaatcaccg gctctttctc gcggctgggc
     2881 tactgatcga agcaggactg gtagacacaa aaacaggcga gctatgctat aaaaaagaca
     2941 ggatattaca agcacttaag gaacttaagt acgatctgga gacatcccca aacccagacg
     3001 cgtaagtgcc tccatccgtg ttccgattcc ctggtgcttc ctcgctcatt cgctcgctac
     3061 gctcggtcat gagactgcgg cgagcactac caccacaatc acgcggaaag ccgcgccatt
     3121 gcagggctga acggggaaaa acggcaaaaa acctgctgct caaaaagacg ccagaaaggc
     3181 gctgttatct gatataggct tatttggtct actctacgag acctcgtttt ttcagttggt
     3241 aataccaggc gcgactgatc cctaatgcct cccacggttt cagcgtgcgt gcagatgtag
     3301 ctactgtgct gcgcttagac ttagaaccgc ccttgcgacc gcgtgcagcc tgaatttctg
     3361 gcgtgtgcgt atcagccaca tactgtgcga aagtttccgg cgtgaagttc ctgtgcgtgt
     3421 atttcgcaat gctcttgcca atagcccgac attcagccag tgaaagcgga acgggaagcg
     3481 atgcattgta catttcgaca cgctggatca ccgcttcaag ccactgtgag aacgctggcc
     3541 agccctgacg aatcgccctg taagcccatt tgcgcgtcat ttcgaacagg tggcagtttc
     3601 gccccatccc gtaatgttta tcgatgctac gacgctctga ggcgctcaaa tcgagataat
     3661 cagccagttc atcgagggta taggcttcct cgcgccactc catcaccagc cattccaggt
     3721 ggaacggatt tttgcaaatc aggccgctgt agttcacatc cgcacaaagt ttctcacaca
     3781 gcgaacgttc aaccgctgcg gcatatttca gcgccttaac cgaggcatca ggcgcggttc
     3841 tcacggcgat gttgagtgcg tagagcaggt gagcgtgtcc gttcacagga tttttaacgg
     3901 tgatgttcgg cgcgggagcg ttccggtcgc tccagtcaat cgcagccccc tcgcggtcaa
     3961 cgtcaaaaac cagccagaac tgcgcatgag gctggttctg ctgtatgtac cgcgcaagaa
     4021 gcgcacgccc tttgccggag atgcgaagac caaaagcgag atcatccgtg tgatagggac
     4081 gatggggtaa attttcgtcg aagtattgaa gcgcggcgct catgtgttac gattctctcc
     4141 gggttatgcg acctacacgc cctctgtatt tcatgttgaa tcttgccgga tctggacatg
     4201 atttcagggg cgtttgtttt tcagtcgctt acactacacc caacggcaaa tcctgtcgaa
     4261 ccttcccgaa aacccgatcc atttaccata actcccgttg tacgcccccc ttaaaacgcc
     4321 ctcagtcgct ttctggcgca aaaaacgcaa aaagacaaga aaacaccagg ccaaaccaga
     4381 aaaacgcgtc agaatcgttt tcatggcgtt gcataactat gcacgaaagc gatgtgcgat
     4441 cggtttcgtg cgttctgaac accgaacggc tcaaaacgac aagttttctc ccctggtgcg
     4501 tggcgctctg acggggtttc ctgtttccaa acttcacatc tcgccaggac aaaaaaaaac
     4561 cgacctgggg tcggtggcaa gaatcagagt ctatgggaaa tattttagtt atcggatgct
     4621 caatattcac aaacgcaaaa aatgcctcag tgatgcccta aaacaacctt tccagaagga
     4681 gtccgcgctt tacgatgcac ggaagagata aaaaacccca caaaagtggg gaaccaagag
     4741 aaacaacaat tacaggttgt tggttgtgtt cgaacaacga tgaagtagct acgctaaata
     4801 ataattaccg tacaggccct acatattcaa cactaaattt aagatcctga cgaaggattt
     4861 ataaatgcac gaaaacacat agacagacaa attcactaaa ttcatacaca aaaacaagtg
     4921 tagttttcta agtaaattag attcgacaac caattagttt atccacatcg cattccactc
     4981 ttgctacacc aatcacattt cttgatatgt aatagcagaa aaaataaaac cagacaccaa
     5041 tagaccaaaa aacaaacatt caacaagaaa cattttgaac aatatcacaa aactgtcaca
     5101 accatcatca gactattgaa aaaaactggt tgctgtttta taaaagcgac tgtaacaacc
     5161 tccact
//
