LOCUS       NZ_CP054347             5631 bp    DNA     circular CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-176 plasmid pSCU-176-2, complete
            sequence.
ACCESSION   NZ_CP054347
VERSION     NZ_CP054347.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14943547
            Assembly: GCF_013315675.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5631)
  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  JOURNAL   Unpublished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 5631)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Hartman,A., Gonzalez,A.,
            Gill,M., Pandori,M. and Hess,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-MAY-2020) Biology, Santa Clara University, 500 El
            Camino Real, Santa Clara, CA 95054, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 100x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 03:58:56
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.5
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,962
            CDSs (total)                      :: 4,848
            Genes (coding)                    :: 4,620
            CDSs (with protein)               :: 4,620
            Genes (RNA)                       :: 114
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 228
            CDSs (without protein)            :: 228
            Pseudo Genes (ambiguous residues) :: 0 of 228
            Pseudo Genes (frameshifted)       :: 88 of 228
            Pseudo Genes (incomplete)         :: 149 of 228
            Pseudo Genes (internal stop)      :: 51 of 228
            Pseudo Genes (multiple problems)  :: 52 of 228
            Pseudo Genes (short protein)      :: 3 of 228
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054347.1.
            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/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..5631
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-176"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-176-2"
                     /geo_loc_name="USA: California"
                     /collection_date="2017"
     gene            complement(join(5396..5631,1..295))
                     /locus_tag="HPE52_RS24430"
                     /old_locus_tag="HPE52_24415"
     CDS             complement(join(5396..5631,1..295))
                     /locus_tag="HPE52_RS24430"
                     /old_locus_tag="HPE52_24415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001673158.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_001673158.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="MbeB family mobilization protein"
     gene            complement(<333..764)
                     /locus_tag="HPE52_RS24985"
                     /old_locus_tag="HPE52_24420"
                     /pseudo=""
     CDS             complement(<333..764)
                     /locus_tag="HPE52_RS24985"
                     /old_locus_tag="HPE52_24420"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial in the middle of a contig;
                     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(973..1296)
                     /locus_tag="HPE52_RS24440"
                     /old_locus_tag="HPE52_24425"
     CDS             complement(973..1296)
                     /locus_tag="HPE52_RS24440"
                     /old_locus_tag="HPE52_24425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /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="WP_024192446.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     AQPLLRQLAAIGNNLNQTARKVNSGQWSSGDRVQVVAALMAIGDELRRLRLAVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1361..1552
                     /locus_tag="HPE52_RS24445"
                     /old_locus_tag="HPE52_24430"
     CDS             1361..1552
                     /locus_tag="HPE52_RS24445"
                     /old_locus_tag="HPE52_24430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165975.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165975.1"
                     /translation="MTKQEKTALNMARFIRGQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENR"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(2755..3621)
                     /locus_tag="HPE52_RS24450"
                     /old_locus_tag="HPE52_24435"
     CDS             complement(2755..3621)
                     /locus_tag="HPE52_RS24450"
                     /old_locus_tag="HPE52_24435"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /GO_function="GO:0005215 - transporter activity [Evidence
                     IEA]"
                     /GO_process="GO:0055085 - transmembrane transport [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="WP_001335763.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     gene            complement(3623..4675)
                     /locus_tag="HPE52_RS24455"
                     /old_locus_tag="HPE52_24440"
     CDS             complement(3623..4675)
                     /locus_tag="HPE52_RS24455"
                     /old_locus_tag="HPE52_24440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557502.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001053268.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPGGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGKGGYSHPEGISTTWHSESNLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIENSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGIPVDDASMFFNSFQPRKFE
                     NKPLYEKEDD"
                     /name="hypothetical protein"
     gene            complement(5156..5389)
                     /locus_tag="HPE52_RS24460"
                     /old_locus_tag="HPE52_24445"
     CDS             complement(5156..5389)
                     /locus_tag="HPE52_RS24460"
                     /old_locus_tag="HPE52_24445"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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="WP_000137437.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          complement(1647..1728)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          complement(2185..2372)
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          complement(4..983)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(5053..5630)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="99.0"
                     /evalue="7.56e-98"
ORIGIN
        1 tcagtactga gacgataatc agccacagcc agcgtttcac gctcattttc agtacggttt
       61 tccagtgcgc gtccatcgta tcgacggtcg ttttctgata cctctccagc agttctttca
      121 gggctgttgt atggtcgttg atagcgttcc tgattaaaga ttcgtttgag gtcagttccc
      181 tgtttacaga ttcttcgagc ttcctgaact cgtcgttcag cattttctct gtagattcgg
      241 ctctctcttt cagctttttc tcgaactccg cgcccgtctg taaaagattg ctcataaaac
      301 gctcctttca gtctgatatt cctcccgccg ttcgggtctg caatgctgat actgcttcgc
      361 gtcaccctga ccacttcaag ccccgcctct gtgagcgcct gaatcacatc ctgacggcct
      421 tttatctctc cggcatggta aagcgcgtct atcccgcgtg tgacgccctc agcaagcgcc
      481 tgtttcgttt ccggcaggtt atcaggaagg gtcagcgtcc ggcggttctc cggggcgttg
      541 gggtcatgca gaccgtaatg gtgattcacc agcgtctgcc aggcatcaat tctcggcctg
      601 tctgcccggt cgtagtacgg ctggaggcgt tttccggtct gtagctccat gttcggaatg
      661 acaaaattca gctcaagccg tcccttgtcc tggtgctcca cccacaggat gctgtactga
      721 tttttctcga gaccgggcat cagtacacgc tcaaagctcg ccatcacttt ttcacgccct
      781 ccaggcggca gctccttctc cgcgaacgac agaacacctg acgtgtattt cttcgcaaat
      841 ggcgtggcat cgatgagttc ccggacctct tccggattcc cctgaagcac cgttgcccct
      901 tcccggttac gctcccttcc cagcaggtaa tcaaccggac cactgccacc accttttccc
      961 ctggcatgaa acttaactat catcccgcgc cccctgttcc ctgaccgcca gacgcagccg
     1021 gcgcagctca tccccgatgg ccatcagtgc ggccaccacc tgaacccggt caccggaaga
     1081 ccactgcccg ctgttcacct tcctcgctgt ctggttaagg ttattcccga tggcggccag
     1141 ctgacgcagt aacggctgtg ccagtgtcgg cagcttcccg gaacgggcaa ccggctcacc
     1201 caggcagacc cgccgcatcc ataccgccag ttgtttaccc tcacagcgtt ccagtaaccg
     1261 ggcatgttca tcatcagtaa cccgtatcgt gagcatcctc tcgcgtttca tcggtatcat
     1321 tacccccatg aacagaaccc ccccttacac ggaggcatca gtgaccaaac aggaaaaaac
     1381 cgcccttaac atggcccgct tcatcagagg ccagacatta acgctgctgg agaagctcaa
     1441 cgaactggac gcggatgaac aggcagacat ctgtgaatcg cttcacgacc acgccgatga
     1501 gctttaccgc agttgcctcg cacgcttcgg ggatgacggt gaaaaccgct gacacatgca
     1561 gctcccggag acggtcacag cttgtctgtg agcggatgcc gggagcagac aagcccgcca
     1621 gggcgcgtca ggccgttgac ctttggggtg tcggggcgaa gccctgaccc agtcacgtag
     1681 cgatagcgga gtgtatactg gcttaaccat tcggcatcag tgcggattgt atgaaaagtg
     1741 cgccatgtcc ggtgtgaaat gccgcacaga tgcgtaagga gaaaatgcca gttcaggcgc
     1801 tcttccgctt cctcgctcac tgactcgcta cgctcggtcg ttcggctgcg gcgagcggac
     1861 tctcctttct caaaaacgct aaccctgtta tccacagaac ccggggataa accaggaaag
     1921 aacatgtgcg caaaaaacga aaccccggga aaggccgcgc cggaggcgct ttttccatag
     1981 gctccgcccc cctgacggac ttcacaaaac agacactttt tcggtgcatc tgtgggagcc
     2041 ttgcggctca accatgaaat ccgccagcgg tggcgaaacc cgacgtggct taaagatcat
     2101 caccgtttcc ggtgaatcgc tccctcctgc gcccccacgt tcccgccata tcgattaccg
     2161 gatacctttt ccgcctttct cccttacggg acacgtggcg ctttctcata gctcacgtct
     2221 tctggtatct cggggcgact taggcagttc gctccgggct gggctgtatg caggaacccc
     2281 ccgttcagcc cgactgctgc gccttctccg gtaactgttc tcttgggtcc aacccggaaa
     2341 agacaccaca aagcgccact ggcagcagcc attggtaaaa gtcatgtgcg agatatttag
     2401 agagtacttg aagtggctgc cggagtgcgg ctacactaga agaacaattt tggtgactcg
     2461 tctcgcataa gacagttacc tggttaagca gtctgcaagc tgacttaacc ttcgatcaaa
     2521 ccgccctgca aggcggtttt ttcgtttaca ggcagcagat tacgcgcaga aaaaaaggat
     2581 ctcaagagga tcctttgatc tttttgttac aaacgtctct atttgactcc cctgagagcg
     2641 ttttagcgcg cctctgaccc ccttggttac attccgacac cagaaacgct cccgtttttt
     2701 acgtgcattt ggcacggtat cgatggaggc cggggggcaa tcctgaacag aatgttactc
     2761 ctctgagtat tttctgttaa gaaaatatac acttagcaca gttacaataa atcctacccc
     2821 ctgtaagaat gtgaattgtt catccaaaaa caaccatgac aaaaataatg caactagcgg
     2881 aataaagtac aacattatcc ctgccaaatg aactgggagc caacgcaagg agttcaagta
     2941 aaaacaaaaa gctaaaaaat attgtaatat tccagatgaa aaaacaataa tcacggattc
     3001 caacggaaga taaattgatg atttagatat aaaaataaag agcgatgaca gtataaggga
     3061 gaatgtcaac tgtccgctca ataatgtgat aggctcaaac gatttaataa ggcgagacga
     3121 tataacaaca taaaatgctg ccgataacac accggcaaca acaagacaat atccaacaat
     3181 attattcgat ccattactga tgtctggcaa ggctaccaaa atactgccaa caattgcacc
     3241 tataaggaac aatataaaat attgcgggga attaatttta actgagcaaa taagaacaga
     3301 caacaccaat ataaacactg attcaagtga aaaaataatt gatgcgcttc ctgctgaaat
     3361 aaaataaagt ccgtagagtg taaaagtata cgctaagaat ggttcaaaaa cgcctgtcgc
     3421 ataagcaagt atcgcttttg agtttaatgg gagttttttt ctttttataa aaagaactat
     3481 ccaagatagt attactgcac tacaaatctg ccagaaaaac acccctccgg catctagttc
     3541 ttcaactcct tttttgctca ttacgatagc tgccccccat gagaacgctg ctaaaaaagc
     3601 aaaaagcatt cctttaatca tattaatcat cctctttctc ataaaggggt ttgttttcaa
     3661 atttccttgg ttgaaaggag ttaaaaaaca tagatgcatc atctacagga ataccaataa
     3721 actctccata ataaggatca tctataggaa actcttctaa tgaaacataa aacaatacat
     3781 tccagttgaa gatcattgga tcactatttt ctatttcatg gagcaatctt tcatccttag
     3841 ttaattctcc tggaattaat acatcagtat gataaaaacc gctgtaataa gaactattac
     3901 cggtgtgcac tgggcatcca aaacgatcca aattagattc tgaatgccat gttgtagaaa
     3961 tcccttccgg atgtgaatac ccacccttac caacagactg aatagtcatg ttacgaatat
     4021 ccgctaacgc ttgttcttga tctttataga aacctttttc tatcgccagc ctcataaaat
     4081 gccccggggc atttacagaa ataagtattc cccctggtat tcttctatca tgatttcttg
     4141 ttctatgagc agaagagtaa aaaacattaa caccagcctt atatattttt agcccatctt
     4201 tatcctgaaa tggtacgctt tcagtataaa taacatcctc ttttattgga tagcactctg
     4261 gcatatgcag cgaacaaata tatttttgta tgtccactaa ctcttctgat ggacgagcaa
     4321 aggcaagttg tggatgaata aaataaatga gatgcgcact gacctctcct cttcttgcgc
     4381 gttctttaaa acgaactctt tcattacgca aaaaatcaaa caaatgacca tcatcattat
     4441 atagttgggg gctatttaca atagataaat ggaaatcaag ccctttaatt ttcttgcttg
     4501 ccaatttacc aaatacacag ggctgattgc ctgacaccca ttttcttagt aaatcttcaa
     4561 ttttatcttt agaagtttcg ttaaagataa atgaatgaat attatcaata tcttttccaa
     4621 atgaaaaact ggatgataat tgtggtagtt tatttatacg ttgttgaaga ttcatgaaag
     4681 ctcccacaag acacctcata tattttttta tatactgaaa ctacattata tttattaccg
     4741 gcgtaaaacg aaataattta ttatcgttac cgatatttta aaaaaatcat tatttgcaca
     4801 gtgttcgagt tgttagtatc actccttcct gaaaatccgc tccatttacc ataacgtcgc
     4861 attgtacgca ccgccaaaac gcgttcggtg cgatcacggc agcagacagg taaaaatggc
     4921 aacaaaccac ccgaaaaact gccgcgatcg cacctgataa attttaaccg catgaatacc
     4981 tatgcaacca gatgctacag gccacattag cccgccttaa tccactgaac acgtcatttt
     5041 tcatggtttc accatcccag cgaagggcca tccagtgtcc gctcctggat ttccggctga
     5101 cgctcccgct ccagagataa ctcatgttcg cgttcctgca tcagccgttc atcccttatc
     5161 tcctgttctc gctgtataac tggctcaagc gttctgtccg ctcgctcaag tgctgcacct
     5221 gctgactcaa ctgcatgact cgcccgttca gcatcgcgtt gtcccgttgc gtaagcgaaa
     5281 acattttctg caattccacg aaggcgttct cccattcgtt cagccgctgc atatagtcct
     5341 gttgcagttg ctctaatgcg ttcagcaaat gtctttccag ctccgtcatg ctctgtcact
     5401 cctgcaccag tctcactgcg ttcagtttgc cgttgtcctt cgtccagttc gtttcggctt
     5461 tcatcccctt cggcaacacc agaaaacgtc cgttgctgtc ctcgtgataa cgcacgcccc
     5521 atgtcttcgc gttcagcttc tccagactct ctttctgctc gcggagaata ttcatattcg
     5581 cgtttatctt catgccctgg taccacagca gactcccggt cgtggcaaac a
//
