LOCUS       CP054331                5635 bp    DNA     circular BCT 10-JUN-2020
DEFINITION  Escherichia coli strain SCU-121 plasmid pSCU-121-3, complete
            sequence.
ACCESSION   CP054331
VERSION     CP054331.1
DBLINK      BioProject: PRJNA624897
            BioSample: SAMN14609781
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 5635)
  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  JOURNAL   Unpublished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 5635)
  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..5635
                     /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-121-3"
                     /geo_loc_name="USA: California"
                     /collection_date="2016"
     gene            99..1151
                     /locus_tag="HHJ34_24425"
     CDS             99..1151
                     /locus_tag="HHJ34_24425"
                     /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="QKN43409.1"
                     /translation="MNLQQRINKLPQLSSSFSFGKDIDNIHSFIFNETSKDKIEDLLRK
                     WVSGNQPCVFGKLASKKIKGLDFHLSIVNSPQLYNDDGHLFDFLRNERVRFKERARRGE
                     VSAHLIYFIHPQLAFARPSEELVDIQKYICSLHMPECYPIKEDVIYTESVPFQDKDGLK
                     IYKAGVNVFYSSAHRTRNHDRRIPGGILISVNAPGHFMRLAIEKGFYKDQEQALADIRN
                     MTIQSVGKGGYSHPEGISTTWHSESNLDRFGCPVHTGNSSYYSGFYHTDVLIPGELTKD
                     ERLLHEIENSDPMIFNWNVLFYVSLEEFPIDDPYYGEFIGIPVDDASMFFNSFQPRKFE
                     NKPLYEKEDD"
                     /name="hypothetical protein"
     gene            1153..2019
                     /locus_tag="HHJ34_24430"
     CDS             1153..2019
                     /locus_tag="HHJ34_24430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001335763.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DMT family transporter"
                     /protein_id="QKN43410.1"
                     /translation="MIKGMLFAFLAAFSWGAAIVMSKKGVEELDAGGVFFWQICSAVIL
                     SWIVLFIKRKKLPLNSKAILAYATGVFEPFLAYTFTLYGLYFISAGSASIIFSLESVFI
                     LVLSVLICSVKINSPQYFILFLIGAIVGSILVALPDISNGSNNIVGYCLVVAGVLSAAF
                     YVVISSRLIKSFEPITLLSGQLTFSLILSSLFIFISKSSIYLPLESVIIVFSSGILQYF
                     LAFCFYLNSLRWLPVHLAGIMLYFIPLVALFLSWLFLDEQFTFLQGVGFIVTVLSVYFL
                     NRKYSEE"
                     /name="DMT family transporter"
     gene            complement(3223..3414)
                     /locus_tag="HHJ34_24435"
     CDS             complement(3223..3414)
                     /locus_tag="HHJ34_24435"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165985.1"
                     /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="QKN43411.1"
                     /translation="MTKQEKTALNMARFIRXQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENX"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3480..3804
                     /locus_tag="HHJ34_24440"
                     /pseudo=""
     CDS             3480..3804
                     /locus_tag="HHJ34_24440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3794..4105
                     /locus_tag="HHJ34_24445"
     CDS             3794..4105
                     /locus_tag="HHJ34_24445"
                     /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="QKN43412.1"
                     /translation="MIVKFHARGKGGGSGPVDYLLGRERNREGATVLQGNPEEVRELID
                     ATPFAKKYTSGVLSFAEKELPPGGREKVMASFERVLMPGLEEKSVQHPVGGAPGQGTA"
                     /name="hypothetical protein"
     gene            4068..4505
                     /locus_tag="HHJ34_24450"
                     /pseudo=""
     CDS             4068..4505
                     /locus_tag="HHJ34_24450"
                     /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            4483..5013
                     /locus_tag="HHJ34_24455"
     CDS             4483..5013
                     /locus_tag="HHJ34_24455"
                     /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="mobilization protein"
                     /protein_id="QKN43413.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLEESVNRELTSNE
                     SLIRNAINDHTTALKELLERYQKTTVDTMDAHWKTVLKMSVKRWLWLIIVSVLMFATTG
                     SLLWYQGMKINANMNILREQKESLEKLNAKTWGVRYHEDSNGRFLVLPKGMKAETNWTK
                     DNGKLNAVRLVQE"
                     /name="mobilization protein"
     gene            5020..5253
                     /gene="mbeD"
                     /locus_tag="HHJ34_24460"
     CDS             5020..5253
                     /gene="mbeD"
                     /locus_tag="HHJ34_24460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137445.1"
                     /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="QKN43414.1"
                     /translation="MTELERHLLNALEQLQQDYMQRLNEWENAFVELQKMFSLTQRDNA
                     MLNGRVMQLSQQVQHLSERTERLSQLYSENRR"
                     /name="mbeD"
     Typing          3047..3128
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="1.3400000000000002e-35"
     Typing          2403..2590
                     /name="rep_cluster_2401"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="4.63e-94"
     Typing          3448..3740
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="97.959"
                     /coverage="83.0"
                     /evalue="8.02e-57"
     Typing          4039..5357
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.864"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tcggtaacga taataaatta tttcgtttta cgccggtaat aaatataatg tagtttcagt
       61 atataaaaaa atatatgagg tgtcttgtgg gagctttcat gaatcttcaa caacgtataa
      121 ataaactacc acaattatca tccagttttt catttggaaa agatattgat aatattcatt
      181 catttatctt taacgaaact tctaaagata aaattgaaga tttactaaga aaatgggtgt
      241 caggcaatca gccctgtgta tttggtaaat tggcaagcaa gaaaattaaa gggcttgatt
      301 tccatttatc tattgtaaat agcccccaac tatataatga tgatggtcat ttgtttgatt
      361 ttttgcgtaa tgaaagagtt cgttttaaag aacgcgcaag aagaggagag gtcagtgcgc
      421 atctcattta ttttattcat ccacaacttg cctttgctcg tccatcagaa gagttagtgg
      481 acatacaaaa atatatttgt tcgctgcata tgccagagtg ctatccaata aaagaggatg
      541 ttatttatac tgaaagcgta ccatttcagg ataaagatgg gctaaaaata tataaggctg
      601 gtgttaatgt tttttactct tctgctcata gaacaagaaa tcatgataga agaataccag
      661 ggggaatact tatttctgta aatgccccgg ggcattttat gaggctggcg atagaaaaag
      721 gtttctataa agatcaagaa caagcgttag cggatattcg taacatgact attcagtctg
      781 ttggtaaggg tgggtattca catccggaag ggatttctac aacatggcat tcagaatcta
      841 atttggatcg ttttggatgc ccagtgcaca ccggtaatag ttcttattac agcggttttt
      901 atcatactga tgtattaatt ccaggagaat taactaagga tgaaagattg ctccatgaaa
      961 tagaaaatag tgatccaatg atcttcaact ggaatgtatt gttttatgtt tcattagaag
     1021 agtttcctat agatgatcct tattatggag agtttattgg tattcctgta gatgatgcat
     1081 ctatgttttt taactccttt caaccaagga aatttgaaaa caaacccctt tatgagaaag
     1141 aggatgatta atatgattaa aggaatgctt tttgcttttt tagcagcgtt ctcatggggg
     1201 gcagctatcg taatgagcaa aaaaggagtt gaagaactag atgccggagg ggtgtttttc
     1261 tggcagattt gtagtgcagt aatactatct tggatagttc tttttataaa aagaaaaaaa
     1321 ctcccattaa actcaaaagc gatacttgct tatgcgacag gcgtttttga accattctta
     1381 gcgtatactt ttacactcta cggactttat tttatttcag caggaagcgc atcaattatt
     1441 ttttcacttg aatcagtgtt tatattggtg ttgtctgttc ttatttgctc agttaaaatt
     1501 aattccccgc aatattttat attgttcctt ataggtgcaa ttgttggcag tattttggta
     1561 gccttgccag acatcagtaa tggatcgaat aatattgttg gatattgtct tgttgttgcc
     1621 ggtgtgttat cggcagcatt ttatgttgtt atatcgtctc gccttattaa atcgtttgag
     1681 cctatcacat tattgagcgg acagttgaca ttctccctta tactgtcatc gctctttatt
     1741 tttatatcta aatcatcaat ttatcttccg ttggaatccg tgattattgt tttttcatct
     1801 ggaatattac aatatttttt agctttttgt ttttacttga actccttgcg ttggctccca
     1861 gttcatttgg cagggataat gttgtacttt attccgctag ttgcattatt tttgtcatgg
     1921 ttgtttttgg atgaacaatt cacattctta cagggggtag gatttattgt aactgtgcta
     1981 agtgtatatt ttcttaacag aaaatactca gaggagtaac attctgttca ggattgcccc
     2041 ccggcctcca tcgataccgt gccaaatgca cgtaaaaaac gggagcgttt ctggtgtcgg
     2101 aatgtaacca agggggtcag aggcgcgcta aaacgctctc aggggagtca aatagagacg
     2161 tttgtaacaa aaagatcaaa ggatcctctt gagatccttt ttttctgcgc gtaatctgct
     2221 gcctgtaaac gaaaaaaccg ccttgcaggg cggtttgatc gaaggttaag tcagcttgca
     2281 gactgcttaa ccaggtaact gtcttatgcg agacgagtca ccaaaattgt tcttctagtg
     2341 tagccgcact ccggcagcca cttcaagtac tctctaaata tctcgcacat gacttttacc
     2401 aatggctgct gccagtggcg ctttgtggtg tcttttccgg gttggaccca agagaacagt
     2461 taccggagaa ggcgcagcag tcgggctgaa cggggggttc ctgcatacag cccagcccgg
     2521 agcgaactgc ctaagtcgcc ccgagatacc agaagacgtg agctatgaga aagcgccacg
     2581 tgtcccgtaa gggagaaagg cggaaaaggt atccggtaat cgatatggcg ggaacgtggg
     2641 ggcgcaggag ggagcgattc accggaaacg gtgatgatct ttaagccacg tcgggtttcg
     2701 ccaccgctgg cggatttcat ggttgagccg caaggctccc acagatgcac cgaaaaagtg
     2761 tctgttttgt gaagtccgtc aggggggcgg agcctatgga aaaagcgcct ccggcgcggc
     2821 ctttcccggg gtttcgtttt ttgcgcacat gttctttcct ggtttatccc cgggttctgt
     2881 ggataacagg gttagcgttt ttgagaaagg agagtccgct cgccgcagcc gaacgaccga
     2941 gcgtagcgag tcagtgagcg aggaagcgga agagcgcctg aactggcatt ttctccttac
     3001 gcatctgtgc ggcatttcac accggacatg gcgcactttt catacaatcc gcactgatgc
     3061 cgaatggtta agccagtata cactccgcta tcgctacgtg actgggtcag ggcttcgccc
     3121 cgacacccca aaggtcaanc ggcctgacgc gccctggcgg gcttgtctgc tcccggcatc
     3181 cgctcacaga caagctgtga ccgtctccgg gagctgcatg tgtcagyggt tttcaccgtc
     3241 atccccgaag cgtgcgaggc arctgcggta aagctcatcg gcgtggtcgt gaagcgattc
     3301 acagatrtct gcctgttcat ccgcgtccag ttcgttgagc ttctccagca gcgttaatgt
     3361 ctggcytctg atraagcggg ccatgttaag ggcggttttt tcctgtttgg tcactgatgc
     3421 ctccgtgtaa ggggggrttt ctgttcatgg gggtaatgat accgatgaaa cgcgagagga
     3481 tgctcacgat acgggttact gatgatgaac atgcccggtt actggaacgc tgtgagggta
     3541 aacaactggc ggtatggatg cggcgggtct gcctgggtga gccggttgcc cgttccggga
     3601 agctgccgac actggcaccg ccgttactgc gtcagctggc cgccatcggg aataacctka
     3661 aycagacagc gaggaaggtg aacagcgggc agtggtcttc cggtgaccgg gttcaggtgg
     3721 tggccgcact gatggccatc gngggatgag ctgcgccggc tgcgtctggc sgtcagggaa
     3781 cagggggcgc gggatgatag ttaagtttca tgccagggga aaaggtggtg gcagtggtcc
     3841 ggttgattac ctgctgggaa gggagcgtaa ccgggaaggg gcaacggtgc ttcagggkaa
     3901 tccggaagar gtccgggaac tcatcgatgc cacgccattt gcgaagaaat acacgtcagg
     3961 tgttctgtcg ttcgcggaga aggagctgcc gcckggaggr cgtgaaaaag tgatggcgag
     4021 ctttgagcgt gtactgatgc ccggtctcga agaaaaatca gtacagcatc ctgtgggtgg
     4081 agcaccagga caagggacgg cttgagctga attttgtcat tccgaacatg gagctacaga
     4141 ccggaaaacg cctccagccg tactacgacc gggcagacag gccgagaatt gatgcctggc
     4201 agacgctggt gaatcaccat tacggkctgc atgaccccaa cgccccggag aaccgccgga
     4261 cgctgacmct ycctgataac ctgccggaaa cgaaacaggc gcttgctgag rgcgtcacac
     4321 gcgggataga cgcgctttac catgccggag agataaaagg ccgtcaggat gtgattcagg
     4381 cgctcacaga ggcggggctt gaagtggtca gggtgacgcg aagcagtatc agcattgcag
     4441 acccgaacgg cgggaggaat atcagactga aaggagcgtt ttatgagcaa tcttttacag
     4501 acgggcgcgg agttcgagaa aaagctgaaa gagagagccg aatctacaga gaaaatgctg
     4561 aacgacgagt tcaggaagct cgaagaatct gtaaacaggg aactgacctc aaacgaatct
     4621 ttaatcagga acgctatcaa cgaccataca acagccctga aagaactgct ggagaggtat
     4681 cagaaaacga ccgtcgatac gatggacgcg cactggaaaa ccgtactgaa aatgagcgtg
     4741 aaacgctggc tgtggctgat tatcgtctca gtactgatgt ttgccacgac cgggagtctg
     4801 ctgtggtacc agggcatgaa gataaacgcg aatatgaata ttctccgcga gcagaaagag
     4861 agtctggaga agctgaacgc gaagacatgg ggcgtgcgtt atcacgagga cagcaacgga
     4921 cgttttctgg tgttgccgaa ggggatgaaa gccgaaacga actggacgaa ggacaacggc
     4981 aaactgaacg cagtgagact ggtgcaggag tgacagagca tgacggagct ggaaagacat
     5041 ttgctgaacg cattagagca actgcaacag gactatatgc agcggctgaa cgaatgggag
     5101 aacgccttcg tggaattgca gaaaatgttt tcgcttacgc aacgggacaa cgcgatgctg
     5161 aacgggcgag tcatgcagtt gagtcagcag gtgcagcact tgagcgagcg gacagaacgc
     5221 ttgagccagt tatacagcga gaacaggaga taagggatga acggctgatg caggaacgcg
     5281 aacatgagtt atctctggag cgggagcgtc agccggaaat ccaggagcgg acactggatg
     5341 gcccttcgct gggatggtga aaccatgaaa aatgacgtgt tcagtggatt aaggcgggct
     5401 aatgtggcct gtagcatctg gttgcatagg tattcatgcg gttaaaattt atcaggtgcg
     5461 atcgcggcag tttttcgggt ggtttgttgc catttttacc tgtctgctgc cgtgatcgca
     5521 ccgaacgcgt tttggcggtg cgtacaatgc gacgttatgg taaatggagc ggattttcag
     5581 gaaggagtga tactaacaac tcgaacactg tgcaaataat gattttttta aaata
//
