LOCUS       CP054456                4082 bp    DNA     circular BCT 14-JUN-2020
DEFINITION  Escherichia coli strain SCU-487 plasmid pSCU-487-2, complete
            sequence.
ACCESSION   CP054456
VERSION     CP054456.1
DBLINK      BioProject: PRJNA624897
            BioSample: SAMN14943541
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4082)
  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  JOURNAL   Unpublished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 4082)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Hartman,A., Gonzalez,A.,
            Gill,M., Pandori,M. and Hess,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-JUN-2020) Biology, Santa Clara University, 500 El
            Camino Real, Santa Clara, CA 95054, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Flye, Unicycler v. 2.6, 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 47x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 06/04/2020 19:09:48
            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)                     :: 4,951
            CDSs (total)                      :: 4,836
            Genes (coding)                    :: 3,774
            CDSs (with protein)               :: 3,774
            Genes (RNA)                       :: 115
            rRNAs                             :: 7, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 1,062
            CDSs (without protein)            :: 1,062
            Pseudo Genes (ambiguous residues) :: 0 of 1,062
            Pseudo Genes (frameshifted)       :: 955 of 1,062
            Pseudo Genes (incomplete)         :: 117 of 1,062
            Pseudo Genes (internal stop)      :: 76 of 1,062
            Pseudo Genes (multiple problems)  :: 83 of 1,062
            CRISPR Arrays                     :: 1
            ##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..4082
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-487"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-487-2"
                     /geo_loc_name="USA: California"
                     /collection_date="2018"
     gene            complement(174..875)
                     /locus_tag="HPE46_24745"
     CDS             complement(174..875)
                     /locus_tag="HPE46_24745"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QKP98215.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCIGRLKSGADAESPKL
                     QKTMTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKDDEKREEFRWIQYRAQY
                     AKGEARAQITFSDAVMPYLTQLQGQFTRVVIKNISRLSRSYSIRIYELLQQFRSTGERI
                     IALDDFRSMLDIEHKYQTYKSLNQQLLRPCIDELNKKSDLAVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1408..1662)
                     /locus_tag="HPE46_24750"
     CDS             complement(1408..1662)
                     /locus_tag="HPE46_24750"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091744.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="mobilization protein"
                     /protein_id="QKP98216.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVIVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobilization protein"
     gene            1841..4000
                     /locus_tag="HPE46_24755"
     CDS             1841..4000
                     /locus_tag="HPE46_24755"
                     /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="QKP98217.1"
                     /translation="MAIYHLSMKIISRNSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHATERRHDRGWSQ"
                     /name="MobA/MobL family protein"
     Typing          complement(1664..1840)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          1841..2199
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(175..875)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          1755..3997
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.866"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 gaagcacaca cataatgcaa gcatagtttt gtttttccgc ccccaaaaaa tgggggttct
       61 tttttcgctg cattagagcg cttttgacgc aatttttcac ttcaatagta ccttcgcact
      121 actaacacaa aaaaaacgca gcagggagcg ttttaggtgc cttaaaatcg attttagatc
      181 gtcatcttga tttgtttgtc ttccttgaag cgaaaatgca gggctacaac cgtgcgcccc
      241 tttttgatcg tctcaaccgt tacagccagg tcgctttttt tgttcagttc gtcaatgcag
      301 ggtcttaata attgctggtt aagtgattta tatgtttgat atttatgctc tatatcaagc
      361 attgagcgaa aatcatcgag agcgataata cgttcgccag tactgcggaa ctgctggagg
      421 agttcgtata tccttatact gtaacttctt gataatctag atatattctt gattacaact
      481 ctagtaaatt gcccttgtag ttgtgtcaaa taaggcatta ctgcgtcaga aaatgttatt
      541 tgtgctctgg cctcgccttt agcgtactgt gcccgatact ggatccagcg gaactcctca
      601 cgtttctcgt catccttgag aatgattgac ctgtcccaca aacgatcaat tgcttcctgt
      661 aactgaacct cggcattttt ccgccccatg tcagggaatg aatcgaaata ttccgcagct
      721 gtaatggtca ttgtcttttg caattttgga gattctgcat cagccccaga cttcaatcga
      781 ccgatgcaaa gtaacaaaaa tcgctgttcc tgtagggtca atttataact ggcttcaacc
      841 agcgcattgg atttataggc aattagatcc gacatagagc atccctcccc aaaaggtaat
      901 gaataaaaga taaacatacc ctcaacgaaa ggcaatgcct ttttatttta atatcccttt
      961 ttctgtgaat attaccttaa atcatattgc ctttacctta aattccccca cctaaacacc
     1021 ttaaatcata ttacctttac cttaaatcac attacctata gcattgtaac attttgtttt
     1081 ctataaggaa ttttggcgct aaaacaagta ttaaaaacaa gatcttaaaa acaagatcta
     1141 aaaacttaac gacgagcctg tggataactt ggagtgctga aaacaaaaaa ccaataaaaa
     1201 caatgcgttg caaaaaagca gaattgcaag ttccgaatac accccctcca accctgtgga
     1261 aatccagtat tcatgcgggt tcagcgcata tcacctcccg aaaaaccgtg cgtatgtgct
     1321 caatcaggcg acggattcac ttccgcttcc tcgcccactc gctcgctaac gctcggtcgc
     1381 tgggactgcg gcgagcggac gatacaatca ctgtcctggc agcgcttcca gctcgttaat
     1441 cagcggcagt atgcgcgtca catcagcctg tcgtgtcacc tctgccttca ggaactggag
     1501 taaccaggca cgcaactgca cctcctccgg ctttctgacc tttgccagca atgctgcacc
     1561 cacaatgacc ttctgcgctg tgtccagact cctgctcttc gcctttaggc gctgtaatct
     1621 ggcctcagca tcagcaatct tctgttcgag tgttctgctc atgatgtaac tccgtgcgcg
     1681 atgaaaaatc gcattttagc gcgtcactgg tagtttaaaa actgagctgg cataatgcac
     1741 ggaaaatcac gaagtgcgca cttatacaat ctccactccg tttcgattgt gtgcgccctg
     1801 cggggctgaa agaaaaccac aaaaaggcat tacggcagaa atggcgattt atcatctcag
     1861 catgaaaatc atctccagaa acagcggcta cagcgccgtt gcttctgctg cctatcgttc
     1921 cggttcactg atgcttgatg agcgtaccgg actgactcac gactacaccc gcaaaagcgg
     1981 tgtggctgaa gctgtgattc tgactcccgc gacagcccct gcctggtgta cgaaccgtgc
     2041 cgaactctgg aatgccgttg agaaggccga acgccggaag aactcacaac ttgcgcggga
     2101 aattgaactc gccatccccc gcgaactacc gcaggatgcc gcacgggaaa ccgttctcgc
     2161 ctttgtcaga gaaaactttg tcagtcaggg catgattgct gatgtggcgt tccatcacat
     2221 ggataaaaca aatccccatg cgcacatcat gctgaccacg agagctgtcg gacctgctgg
     2281 attcggtgga aaggtcaggg actggaacga ccggacacat gccgagacgt ggcgtgcatc
     2341 atgggctgac catgcgaaca gggcactggc gaacgccggt tatcaggaag agatagacca
     2401 tcgttcatac gagcgacagg ggcttgagaa aacgcctggt attcacctcg gaaagtctgc
     2461 ctgtgcgatg gaaacacgcg gtatcgaaac agaacgcggc gaacagaatc gtctgattaa
     2521 cagacttaac ctggaaatac agatttcccg taccgaactc agaaacagcg ggctgacaga
     2581 gcctgcccgc cgtgtggctg accttctgaa tatcgtgctt cctgacaacg caacttcgta
     2641 cacactacgt gacatcatcg aagcgttgcc gaaggacagt aatgcggcat ggaaactcac
     2701 cagtaatgcc atgtcgatga tggcagatat gcaggcgacg cgcagacgct gggaagagct
     2761 gaacaccgaa cgaaaggaag cgatgagcca tgctgccagc ctgaaaaaat catcgccgtt
     2821 ttcgtccggt ttttcccgta ttcccctgat gcaatgggcg gcaccggaat accgtagcga
     2881 acagggaaaa atccagtcgc tgagccagca aatggaaaaa ttgcgacagc attaccggaa
     2941 ggtggagaaa caggacattc ccgcgagtca gacggcattt gaaaaacagt ggcagcagtg
     3001 gggggcatcc ggccttgcag ctctcagagt ccagttgctt aaacgtgaag aggaattgcg
     3061 ccggaaggag caggaggata cagaacgtag tcgcgcggag cgacgagcgg aacagctcag
     3121 gaaaaatgac aatgccgtta tggattcagg ggtactgagc gcagtcgtta cggggtatgg
     3181 cgaggccccc atgcctggta acggggaaat gacctgttac cttctgcttc acaaccggaa
     3241 cggagaatac acgctctggg ggaacgagct ggagaaatac cgcaccagaa tctttgagcg
     3301 tgttgattta atgcgtgaca ggagtggtta tatctgtgac cgaagcgaaa tcggtcaaca
     3361 tccaccactg caacgtgttt attcctctgc gacctttgag caacttctga cgcaggtttg
     3421 ccagacatgg ccgcaatata cccgcaatct ccgccagccg aagacatggc cggagtcttt
     3481 ctgtcttgga gaagaccgcc agccagccat gccatcactg gcagcaagga aggtggattt
     3541 tacgcaggga cgtctgctac cgacgctgat gccggtaatg agttctgtcg accgggaaac
     3601 ccgccagctt cagcttttgc tggtcatggg cgtggatgac tctctgggcg gtgttgtccg
     3661 gcttaatggt acgctgtatc ccgcgtttgc cgttccctca gccgataaca gccagctggt
     3721 catcagtgca ctgaccgata aggggttacg gtatgcaggg tatggtgttg ccgtaaatca
     3781 cgatgcagac agccacatat cacctgcgcc ggaacttatg gagtttcatc tgaaaacccg
     3841 tgaggcaccg ctttttgctg ccgtcaacac accagaaaaa cagccggatc atctgttccg
     3901 ctcgctgggt tttaatcgta cctgggacga atggcggcgc gaggaagatg cacgaacaca
     3961 cgccaccgag aggagacatg atcgcggttg gtcacagtga atgtgaacaa tattttgttt
     4021 tgtttaacat cgtgttatgt tcgtcgatgt tcttcgatgt tcatcgacag ggatgaatgc
     4081 aa
//
