LOCUS       CP054332                4091 bp    DNA     circular BCT 10-JUN-2020
DEFINITION  Escherichia coli strain SCU-121 plasmid pSCU-121-4, complete
            sequence.
ACCESSION   CP054332
VERSION     CP054332.1
DBLINK      BioProject: PRJNA624897
            BioSample: SAMN14609781
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4091)
  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  JOURNAL   Unpublished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 4091)
  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..4091
                     /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-121-4"
                     /geo_loc_name="USA: California"
                     /collection_date="2016"
     gene            complement(456..746)
                     /locus_tag="HHJ34_24465"
     CDS             complement(456..746)
                     /locus_tag="HHJ34_24465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001514113.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein"
                     /protein_id="QKN43415.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVREP
                     GETQLRAWLLHLLKTEVTRQADVSRIQPLIDELNALPKPVPKEVSENDQQA"
                     /name="mobilization protein"
     gene            917..3064
                     /locus_tag="HHJ34_24470"
     CDS             917..3064
                     /locus_tag="HHJ34_24470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016240513.1"
                     /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="QKN43417.1"
                     /translation="MAIYHLSMKILSRSKGYSAVASAAYRAGEKILDERTGVIHDYTRK
                     NGVASAVILTPANAPAWCANRAELWNAVEKAERRKNSQLAREFELAIPRELAQDAARET
                     VLNFVRENFVSRGMIADVAFHNLGGSNPHAHIMLSMRAITPDGFGEKVREWNDWTHAET
                     WRGSWADHANRALANAGYQEEIDHRSYERQGVEKTPGIHLGKSACAMEKWGIETERGEQ
                     NRLINRLNLEIQVSRDELRNSELTEPARRMADLLNIELPDNATSYILHDIIEALPTDSN
                     AAWKLTSKAMSMMADMQATRRRWEDLNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWV
                     APEYGREQEKIQSLSQRMEKLRQHHWKVEKQDIPASQKAFETQWQQWGASGLADLREQL
                     RKREEELRRKEQEETERRRAEQLRRNDNAVMDSGVLKAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRSRIFESVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSMGGVVRLNGTLYPAFAVPTADNSQLVINALTDKGLRFA
                     GYGEAVNHDADSPARPAPELMQFHLKTWSEPLFAIVNTPEKQPDHLFRSLGFERTWDEW
                     QRDEYARTHATERRHDRGWSQ"
                     /name="MobA/MobL family protein"
     gene            complement(3313..4014)
                     /locus_tag="HHJ34_24475"
     CDS             complement(3313..4014)
                     /locus_tag="HHJ34_24475"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011666799.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QKN43416.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCIGRLKSGSDAESTEL
                     QKTMTVTAEEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQY
                     AKGEGKAQITFSDAVMPYLTQLKGQFTRVVIKNISNLSRSYSIRIYELLQQFRSTGERI
                     IALDDFRSMLDIEHKYQTYKSLNQQLLRPCVDELNQKSDLAVTLETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(751..901)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.81"
                     /coverage="85.0"
                     /evalue="3.53e-55"
     Typing          complement(918..1272)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3315..4014)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="89.301"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          876..3061
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.177"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 atcccttttc ctgtgaatat taccttaaat catattgcct ttaccttaaa tcatattgcc
       61 tatccacctt aaatcatatt gcctttacct taaattatat tacctatagt cttctaaact
      121 cttgaatttc ataagaaaat tcgaccctaa aacaagtatt aaaaacaaga tcttaaaaac
      181 aagatctaaa aacttaacgg cgagcctgtg gaaaacttgg ggggttcaaa acaaaaaatc
      241 atggaaaaca acaggttaca aaaaagcagg ttcgcaagct ttagcaaaac cccgctcaac
      301 cctgtggaaa tccagtattc atgcgggttc agcgcatatc acctgtcgaa aaaccgtgcg
      361 tatgtgctca atctggcgac ggattcactt ccgcttcctc gcccactcgc tcgctaacgc
      421 tcggtcgctg gggctgcggc gagcggacgg tgcattcacg cctgttggtc gttttctgac
      481 acttctttgg ggactggttt tggtaacgcg ttcagttcgt caatcaacgg ctgtatcctg
      541 ctcacatcag cctgccgtgt tacctctgtc ttcaggagat gaagcaacca ggctcgtagt
      601 tgtgtttccc caggctccct gacctttgcc agcaatgccg ctcccacaat gaccttctgc
      661 gctgtgtcca ggctcctgct cttcgccttc agacgctgca atctggcctc agcatcggca
      721 atcttctgtt cgagtgttct actcattccg taactccgtg cgcggtgaaa aatcgcattt
      781 tagcgcgtca ctggtagttt aaaaactgaa ctggcataat gcacagcaaa tcacgaagtg
      841 cgcacttata caaactctcc ttcgtcgagt ttgtgtgcgc cctgcggggc taaaagaaaa
      901 cggcaacaac gacacgatgg caatttatca tctcagcatg aagattcttt ccagaagcaa
      961 gggctacagc gccgttgctt ctgctgccta tcgtgccgga gaaaaaatac tggatgagcg
     1021 caccggagtg attcacgact acacccgcaa aaacggtgta gccagcgcag tgattctgac
     1081 gccagcaaac gccccagcat ggtgtgcgaa ccgcgccgaa ctctggaatg ctgttgaaaa
     1141 agccgagcgg cggaaaaact cacaacttgc gcgggagttc gaactcgcca tcccccgtga
     1201 actggcgcag gatgccgcac gggaaacagt tctcaacttc gtaagggaaa actttgtcag
     1261 tcgcggcatg atcgccgacg tggcctttca caatctgggc gggtcaaacc cacacgcgca
     1321 catcatgcta tccatgaggg caatcacgcc tgacggcttc ggggagaaag tccgtgagtg
     1381 gaatgactgg actcacgccg aaacatggcg gggatcatgg gcagaccatg cgaacagggc
     1441 gctggcgaac gccggttatc aggaagagat agaccatcgt tcatacgagc gacagggggt
     1501 tgagaaaacg cctggcattc acctcggaaa gtcggcctgt gcgatggaaa agtggggcat
     1561 cgaaacagaa cgcggcgaac agaatcgcct gattaacagg cttaacctgg aaatacaggt
     1621 ttcccgcgac gaactcagga acagtgagct gacagagccc gcacgccgta tggctgacct
     1681 tctgaatatt gagcttcctg acaacgcaac ttcgtacata ctgcatgaca tcatcgaagc
     1741 gttgccgacg gacagtaacg cagcatggaa actcaccagt aaagccatgt cgatgatggc
     1801 agatatgcag gcgacgcgca gacgctggga agatctgaac accgaacgaa aggaagcgat
     1861 gagccatgct gccagcctga aaaaatcatc gccgttttcg tccggttttt cccgtattcc
     1921 cctgatgcaa tgggttgcac cggaatacgg ccgcgaacag gaaaaaatcc agtcgttgag
     1981 ccagcgcatg gaaaaattgc ggcagcatca ctggaaggtt gagaaacagg acattcccgc
     2041 gagtcaaaaa gcatttgaaa cacagtggca gcagtggggt gcatctggcc ttgcagatct
     2101 ccgagaacag ttgcgtaaac gtgaagagga attgcgccgg aaggagcagg aggaaacaga
     2161 acgtcgtcgg gcggagcagc tcaggagaaa tgacaatgcc gttatggatt caggggtact
     2221 gaaagcagtc gttacggggt atggcgaggc ccccatgcca ggtaacgggg aaatgacctg
     2281 ttaccttctg cttcacaacc ggaacggaga atatacgctc tgggggaacg agctggagaa
     2341 ataccgctcc agaatttttg agagtgttga tttaatgcgt gacaggagtg gttatatctg
     2401 tgaccgaagc gaaatcggtc aacgtccacc actgcaacgt gtttattcct ctgcgacctt
     2461 tgagcaactg ctgacgcagg tttgccagac atggccgcaa catacccgta atctccgcca
     2521 gccgaaaaca tggccggagt ctttctgtct tggagaagac cgccagccag ccatgccatc
     2581 actggcggca aggaaggtgg attttacgca gggacgtctg ccaccgactc tgatgccggt
     2641 aatgagttct gtcgaccgtg aaacccgcca gcttcagctt ttgctggtca tgggtgtgga
     2701 tgactctatg ggcggtgttg tccggcttaa tggtacgctg tatcccgcgt ttgccgtccc
     2761 cacagccgac aacagccagc tggtaatcaa tgcactgacc gacaaaggtt tacgctttgc
     2821 aggctatggt gaagcggtaa accacgatgc tgacagtccg gcacgtcctg cgccggaact
     2881 tatgcagttt catctgaaaa cctggagcga accgcttttt gctatcgtca acacgccaga
     2941 aaaacagccg gatcatctgt tccgctcgct gggctttgag cgcacctggg atgaatggca
     3001 acgtgatgaa tatgcccgaa cacacgccac cgagaggaga catgatcgcg gttggtcaca
     3061 gtgaatgtga ccaatatttt gttttgttta acatcgtgtt atgttcgtcg atgttcatcg
     3121 acagggatga atgcaagaag cacacacata acacaaatca actttatagt tttcccgccc
     3181 ccgaaaaatt gggggttctt ttttcactgt gccagagcgt ttatgacgca attttttact
     3241 tcaccagtac cttcgcatgc caaacacaaa aaaaacgcgt cagagagcgt tttagaggcc
     3301 ttaaaatcga ttctagatcg tcatcttgat ctgtttgtct tccttgaagc gaaaatgcag
     3361 ggctacaacc gtgcgcccct tcttgatcgt ctcaagcgtt acagccaagt cgcttttttg
     3421 attcagttcg tcaacgcaag gtcttaataa ttgctggttc agagacttat atgtttgata
     3481 tttatgctct atatcaagca ttgagcgaaa atcatcgagg gcgataatac gttcccctgt
     3541 gctgcggaat tgctggagaa gttcgtatat tcttatgctg taacttcttg ataaattgga
     3601 gatgttctta attacaactc tagtaaattg ccccttcaac tgtgtcagat aaggcatgac
     3661 cgcatctgaa aaagtgattt gggctttgcc ctcaccttta gcgtactgtg cccgatactg
     3721 gatccagcgg aactcctcgc gcttctcatc gtccttaagg atgatcgacc tgtcccacaa
     3781 acgatcaatt gcttcctgta gctgaacctc ggcatttttc cgccccatat cagggaatga
     3841 gtcgaaatac tcttcggcgg taacagtcat ggtcttttgc aattcagtgg attctgcatc
     3901 agaacccgac ttcaatcgac caatgcaaag taacaagaat cgctgttcct gaagagtcaa
     3961 tttatagctg gcctcaacca gtgcattgga tttgtaggca atcagatccg acattgtaaa
     4021 tccctcaacc taaggtaatg agtaaaatat aaacattcct ttaggtaaag gcaatatgat
     4081 ttaattttaa t
//
