LOCUS       CP054340                4773 bp    DNA     circular BCT 10-JUN-2020
DEFINITION  Escherichia coli strain SCU-120 plasmid pSCU-120-5, complete
            sequence.
ACCESSION   CP054340
VERSION     CP054340.1
DBLINK      BioProject: PRJNA624897
            BioSample: SAMN14609780
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4773)
  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  JOURNAL   Unpublished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 4773)
  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..4773
                     /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-120-5"
                     /geo_loc_name="USA: California"
                     /collection_date="2016"
     gene            40..591
                     /locus_tag="HHJ33_26565"
     CDS             40..591
                     /locus_tag="HHJ33_26565"
                     /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="QKN47625.1"
                     /translation="MKDMKAVVVFTGKDLNIMRTEGGSGYWHARTDRLNDADYLIAVRN
                     RRETWAVKDLEHGTAFLIAKITGCFKSPDYDDRNVITFDEYAEIHTPKAWKMLTDGQRY
                     PVAYLSAQEAFLRIGVTPEQLEWKKFHPSSPSVPNTVIPGLAEEKTEKLSLNEAIERAK
                     KDISNATGIDSSAITISIKI"
                     /name="hypothetical protein"
     gene            complement(790..1005)
                     /gene="mbeD"
                     /locus_tag="HHJ33_26570"
     CDS             complement(790..1005)
                     /gene="mbeD"
                     /locus_tag="HHJ33_26570"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="QKN47626.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMFGLMQRENA
                     ALSERVTGLSRQVQSLSEQLRRLSQG"
                     /name="mbeD"
     gene            complement(1009..1494)
                     /locus_tag="HHJ33_26575"
     CDS             complement(1009..1494)
                     /locus_tag="HHJ33_26575"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_012565228.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein"
                     /protein_id="QKN47627.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTGEMLKVAFSEHEKFVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSTLLTASGASILWWQGQQIL
                     DNYTIIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="mobilization protein"
     gene            complement(1469..2233)
                     /locus_tag="HHJ33_26580"
                     /pseudo=""
     CDS             complement(1469..2233)
                     /locus_tag="HHJ33_26580"
                     /inference="COORDINATES: protein motif:HMM:NF015397.1"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            complement(2172..2516)
                     /locus_tag="HHJ33_26585"
     CDS             complement(2172..2516)
                     /locus_tag="HHJ33_26585"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006122514.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="QKN47628.1"
                     /translation="MSEKRNKMLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLAEKPAR
                     AGKLPSISPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHA
                     VLEKGADDDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2775..3108
                     /locus_tag="HHJ33_26590"
                     /pseudo=""
     CDS             2775..3108
                     /locus_tag="HHJ33_26590"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229779.1"
                     /note="frameshifted; incomplete; partial on complete
                     genome; missing N-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            3133..3216
                     /locus_tag="HHJ33_26595"
     CDS             3133..3216
                     /locus_tag="HHJ33_26595"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QKN47630.1"
                     /translation="MHEPPVQSDRCALSGNYRLESNPDRHD"
                     /name="replication initiation protein"
     gene            complement(3810..4277)
                     /locus_tag="HHJ33_26600"
     CDS             complement(3810..4277)
                     /locus_tag="HHJ33_26600"
                     /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="QKN47629.1"
                     /translation="MPAPNNYGVAGSPNSAIAHPDGLDCYGRVPEINSKGDVIPAGDIF
                     LRVGRHTGPNRGFGVRHIWAEHEQELVKLGYTTVNDVARFVRDIIRRGVPIYCEFNSTS
                     GKHRPAVLKSSVGIVILEPREAPETESGWIYVVVTAYTRRTAHGTLVGHIE"
                     /name="hypothetical protein"
     Typing          complement(2597..2784)
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.864"
                     /coverage="87.0"
                     /evalue="5.83e-49"
     Typing          2730..3242
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="92.829"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(687..2182)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.385"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 taaaaaaatg aaattgactc acctattaag ggtttctata tgaaagatat gaaagctgtt
       61 gtggttttta ccgggaagga tttgaacata atgagaaccg agggggggtc aggctactgg
      121 catgccagaa cagacaggct caacgatgcc gattacctca tagcagtaag aaacagaagg
      181 gaaacgtggg cagtaaaaga cctggaacac ggcacagcat tcctgatcgc caaaattacc
      241 gggtgtttta aaagccctga ttacgacgac aggaacgtca taacctttga tgaatacgca
      301 gaaattcaca ctccaaaagc atggaaaatg ctaaccgatg gtcagcgcta tccggttgct
      361 tacctgagcg cacaggaagc ttttttacgt attggggtaa caccggaaca actggaatgg
      421 aagaaattcc atccttcatc cccatcggtt cctaatacag tgattcctgg tctggctgaa
      481 gagaaaacag aaaaactctc ccttaacgag gcaattgaaa gagccaaaaa ggatattagc
      541 aacgcaacag ggattgatag ctcagccata acaataagca tcaagatctg atgaagcgtg
      601 aacaacaaga tagcagcctc atgttctaga actgaacctg tgcgccagaa acagcaagcc
      661 catgcttttc cggcgcacag attcaaagtg acggaccgtt gtacgttcgc tgtcgctgag
      721 atcgttccag ctccagcgct ttctgatgct gcgccgcccg ttcctgctca cgatgtgcct
      781 ctatcacgtt cagccttgtg acaaccggcg cagctgctcg ctcaaactct gcacctgcct
      841 gctcaagccc gtgacgcgct cgctcagcgc cgcgttctcc cgttgcataa gaccaaacat
      901 cgtccgccat tccgcgaagg cgttctccca ctcgtccagc cttttcgagt agtcctgctg
      961 tagctgctct aatgcgctca gcaactgttt ttccagctcc gtcatgtgct atttccccgc
     1021 cagtatcatc cagctcgaat cctctccgaa ccgtcccgct tccgggttca ccctcacgca
     1081 gcgccgtctc tgctctccgc aggtcgagag ctgcacgccg ctgttcctct cggacagcat
     1141 ggcctgcgtg ctcttctgct cccggatgat cgtgtaattg tcgagtatct gctgcccctg
     1201 ccaccataga atgcttgcgc ccgatgctgt cagcagtgta gacaccagga cgatggtcag
     1261 ccacgtctgg ctgaccatac gcaccatgcc tttcgtgcgc tggctcatgg ctgaggacag
     1321 cttccggtcg tggtcgagga tggcggcgct gattctcttc tcgctttcgc tcagttccgc
     1381 tctgacaaac ttctcgtgct cgctgaatgc gactttcagc atctcgccgg tactctgctg
     1441 ctgcgctttc gatttctgct ctaagtcctt cgccagcgtt aaaagactgt tcatagatgg
     1501 ctcccttcag tcggatgttt cgccccccgt ccgggtcggc aatgctgatg ctgctttttg
     1561 tggtgcgcac cacctcaaaa cctgcgcttt ctagcgcctc agtgacgtcc tggcgggttt
     1621 tcagctcccc ggacgaggct aaggccagta aaccccgtgt aattgcctga gcggcttcct
     1681 gcttcgtttt cggcagcgcg gacggcgtga ccagcgcccg ccggttttca ggcgcgttcg
     1741 ggtcatgcag ccccagcctg ccgttcacga tggtctgcca ggcatcaatg cgcggacggt
     1801 cggcgcggtc gtaatacggc tggagacgcc tgcctgtcag cagctccatg ttcgggatca
     1861 ggaagttcag ctccagccgc cccttatcct ggtgctcaac ccatagcacg ctgtactggt
     1921 ctttatcgag tccgggcatc agaacccgtt caaagctcgc catcagcttt tcgcgctgcc
     1981 cgggcggtaa atccttttcg gcaaaggaca ggacgccgga tgtgtacttt tttgcgtagg
     2041 gcgaggcgtc gataagctcc ctgacttctt ccggcttccc ctgcagaacg gtggcgccgt
     2101 cgcgctgtcg gtctttcccc agcagataat ccaccggacc ggcgccaccg ccgcgccctc
     2161 gcgggtgaaa cttaacgatc atcgtctgca cccttttcca gcacggcatg ccgcagccgc
     2221 tcgagtccgg catctatggc catcagcgcg gcgacgacct gcacgcggtc gtgcccgctg
     2281 ccgccaccgg cgttaacctg ccgggcaatc tggttgaggt tattccccat gccggcaagc
     2341 tgacgaagca gcgccggcga gattgaggga agcttgccgg cgcgggcggg tttctcggcc
     2401 aggcacgtct ggcgcatcca ggctgcaagc tgtttaccgt cgcagcgttc cagcagacgg
     2461 cggtgctcat cttcggtcac ccacatggtg agcatcttgt tccgtttctc tgacaaaccg
     2521 atctcctgat aacgccggga cgggcgggaa atcttttccc ggtcggcgcg gtgttggaca
     2581 agccgcaggc gcgtcagtgg ttttagcagg tttcggggcg cagccctgaa ccagtcacgt
     2641 agcgctagcg gagtgtatac tggctcaata tgttacggcg gagtaacacg taatgaaagt
     2701 gcttcatgtg gcaggggaaa aatgcagctg cagggcgtac aggagaaaat ggaggttacg
     2761 gtgatatgac gcctcctcgc tcactcggtc gcttccgctc ctgacgttcg gctgcggcgg
     2821 gcgttacctg caaacggata agagcaaagg catacggcat ggcaagcagg acaggaaaag
     2881 gatgcggcgc tgccgttttt ccataggctc cgcccccctg acaagcatca cgaaatctga
     2941 cgctcaaatc agtggtggcg aaacccgaca ggacttaaag ataccaggcg tttccccctg
     3001 gtggctccct cgtgcgctct cctgttcctg cctttcggtt taccggtgtc attccgctgt
     3061 tatggccgcg tttatctcat tccacgcctg acactcagtt ccgggtaggc agttcgctcc
     3121 aagctggact gtatgcacga accccccgtt cagtccgacc gctgcgcctt gtccggtaac
     3181 tatcgtcttg agtccaaccc ggatagacac gactaatcgc cattggcaac ggccactggt
     3241 aagcaggatg tgcgagagat gtaacgagag ttcttgaagt ggcggcctaa ctgaggctac
     3301 actgaaagga cagtatttgg tgacatgtct cgcacaagac tgttaccacg gttagagaat
     3361 ctgccaggat taactaacct tcgaaaaaac cacctgccag ggtggttttt tcgtttctga
     3421 gcaagagact acgacgagcc actgatgatc tcaagtgttc atttctgata ttcacagcag
     3481 aataactgtt aggatatagg gtatctatag ccaggagctt caagaaatcc agacacagca
     3541 atggattcca gggttatcga aaaaaattag tatataggtt gcaaccaaaa tgttggttgc
     3601 aaatctacat cacgatgttt atgattattg tactgcaaga gcattcgcag ggggcatcaa
     3661 ccagtaatag gccttctgtg ccgggcagtc agatggctgg tcatctgccg ggtagttacg
     3721 acaagcgtcg gtttctgaac cctatgtgct aaggaaatgc tgcgactacc aacgaattca
     3781 taaagggcgc tttttagcgc cctatttttt tattcaatat gaccaaccaa agtaccgtgc
     3841 gccgtccttc gtgtgtacgc agtcacaacg acatagatcc aacctgactc agtttcaggc
     3901 gcttctctgg gctcaagaat tacgatgcct accgacgact ttagcactgc aggccgatgt
     3961 ttaccgcttg tactgttgaa ctcgcaatat attggtacgc cacgacgaat aatatcccgg
     4021 acaaaacgag ccacatcatt aacggtcgta tatcccagct taaccagttc ctgctcgtgc
     4081 tcagcccaga tatggcgaac accaaagccc cggttagggc cagtatgcct accaacacgc
     4141 aagaagatgt cgccagcagg aataacatca cctttagaat taatttcagg gacacggcca
     4201 tagcaatcaa gcccatcagg gtgagctata gcgctgttag gtgaaccagc tacaccgtaa
     4261 ttgtttggag caggcacaaa acgatcctta ttgagtagag tccgcatatg gtaccagaga
     4321 ggaaacaagc ggaaggagcc caagaaaaaa gcagagacga taaaaagaat ccttatggat
     4381 tatttttttg tcctttcatc cttggcgcat aaggatatca cacctgaaaa tgtgacgtgc
     4441 gaatcgccct agcagctaga tttaccataa catcccttgc ccgcaccgct ccggacgggt
     4501 tcagcgtgaa agcggcgtta gcccggtaaa gccggcagta aactccccgc taaaccgcgc
     4561 attctgcgcc tgataaattt cacgcggctg catagccatg cagccacgtg aatggctcat
     4621 gctttcaatg tatatcctcg tccaagcccc tgttttaacc ggtttatcaa aaaaacaaac
     4681 aggaagcctt atcactaaca ataaaagagg tagggggctg cattttatcg cataaaaaac
     4741 atttacaaca cgaattctat cgtatagatt tca
//
