LOCUS       CP054323                4072 bp    DNA     circular BCT 10-JUN-2020
DEFINITION  Escherichia coli strain SCU-390 plasmid pSCU-390-4, complete
            sequence.
ACCESSION   CP054323
VERSION     CP054323.1
DBLINK      BioProject: PRJNA624897
            BioSample: SAMN14609796
KEYWORDS    .
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4072)
  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  JOURNAL   Unpublished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 4072)
  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                   :: 13x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI
            Annotation Date                   :: 05/26/2020 18:17:01
            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)                     :: 5,020
            CDSs (total)                      :: 4,901
            Genes (coding)                    :: 3,691
            CDSs (with protein)               :: 3,691
            Genes (RNA)                       :: 119
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 91
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 1,210
            CDSs (without protein)            :: 1,210
            Pseudo Genes (ambiguous residues) :: 0 of 1,210
            Pseudo Genes (frameshifted)       :: 1,101 of 1,210
            Pseudo Genes (incomplete)         :: 108 of 1,210
            Pseudo Genes (internal stop)      :: 59 of 1,210
            Pseudo Genes (multiple problems)  :: 54 of 1,210
            ##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..4072
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-390"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-390-4"
                     /geo_loc_name="USA: California"
                     /collection_date="2018"
     gene            complement(494..748)
                     /locus_tag="HHJ49_25080"
     CDS             complement(494..748)
                     /locus_tag="HHJ49_25080"
                     /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="QKN36154.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPEQ"
                     /name="mobilization protein"
     gene            927..3074
                     /locus_tag="HHJ49_25085"
     CDS             927..3074
                     /locus_tag="HHJ49_25085"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001557504.1"
                     /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="QKN36156.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAERRKNSQLAREIELAIPHELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAIGPAGFSGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNGGLTEPARRVADLLNIGLPDNATSYTLRDIIEALPKDSN
                     SAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQMAFEKQWQQWGESGLAALRAQL
                     LKREEELRRKEQEDTERSRAEQLRKNDNAVMDSGVLRAVVTGYGEAPMPGNGEMTCYLL
                     LHNRNGEYTLWGNELEKYRTRIFESVDLMRDRSGYICDRSEIGQRPPLQRVYSSATFEQ
                     LLTQVCQTWPQHTRNLRQPKTWPESFCLGEDRQPAMPSPAARKVDFMQGRLPPTLMPVM
                     SSVDRETRQLQLLLVMGVDDSLGGVIRLNGTLYPAFAVPSADNRHLVISALTDKGLRYA
                     GYGVAVNHDADSHISPAPELMQFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRTWEEW
                     QREEDARTHTTERRHDRGWSQ"
                     /name="MobA/MobL family protein"
     gene            complement(3332..4033)
                     /locus_tag="HHJ49_25090"
     CDS             complement(3332..4033)
                     /locus_tag="HHJ49_25090"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281396.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="QKN36155.1"
                     /translation="MSDLIAYKSNALIEASYKLTLQEQRFLLVCISRLKSGEDSPSPDE
                     QKTMTITAAEFHDAFPDMGRQHAEARLKEAIDRLWDRSVIIKNEEKREEFRWVQYRAQY
                     FKGEAKVDITFSDAIMPYLTQLKGQFTRVVVKNVSSLSSTYSIRIYELLQQFRSTGDRT
                     IAIDDFRTMLAVEDKYQQFKDLNKMIIKPAIAELNEKSDLVVTVETIKKGRTVVALHFR
                     FKEDKQIKMTI"
                     /name="replication initiation protein"
     Typing          complement(750..926)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.61e-88"
     Typing          927..1285
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(3333..4033)
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="99.858"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          841..3071
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="95.989"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 acgccactta tcatatgggt ggaagttttt tttttgcaac cccctttttc tgtggattac
       61 acccccaaaa gctccacctt tcacccccaa aagctccacc tttcaccccc aaaagctcca
      121 cctttcaccc ccaaaagctc cacttatctt gccagaacat ctttaaaatc atggtgttac
      181 aagacctaaa aaggttttaa aaaaaagatc taaaaataag atcttaaaaa cttaacggcg
      241 agcctgtgga taacttgggg tgctgaaaac aaaaaaccaa taaaaacaat gcgttgaaat
      301 aaagcagaat tgcaagtttc gaatacaccc cctccaaccc tgtggaaacc cagtattcat
      361 gcgggttcag cgcatatcac ctgccgaaaa accgtgcgta tgtgctcaac ctggcgactg
      421 attcacttcc gcttcctcgc ccactcgctc gctaacgctc ggtcgctggg gctgcggcga
      481 gcggacgata caatcactgt tctggcagcg cctccagctc gttaatcagc ggcagtatgc
      541 gcgtcacatc agcctgtcgt gtcacctctg ccttcaggaa ctggagtaac caggcacgca
      601 actgcacctc ctccggcttt ctgacctttg ccagcaatgc agcacccaca acaaccttct
      661 gcgctgtgtc caggctccgg ctcttcgcct tcaggcgctg taatctcgcc tcagcatcag
      721 caatcttctg ttcgagcgtt ctgctcatga tgtaactccg tgcgcgatga aaaatcgcat
      781 tttagcgcgt cactggtagt ttaaaaactg agctggcata atgcacggca aatcacgaag
      841 tgcgcactta tacaatctcc actccgtttc gattgtgtgc gccctgcggg gctgaaagaa
      901 aactacaaaa aggcattacg gcagaaatgg cgatttatca tctcagcatg aaaattatct
      961 ccagaagcag cggctacagc gccgtagctt ccgctgccta tcgttccggt tcactgatgc
     1021 ttgatgagcg taccggactg actcacgact acacccgcaa aagcggtgtg gctgaggctg
     1081 tgattctgac ccccgccacc gcccctgcct ggtgtacgaa ccgtgccgaa ctctggaatg
     1141 ccgttgagaa ggccgaacgc cggaagaact cacaacttgc gcgggaaatt gaactcgcca
     1201 tcccccacga actgccgcag gatgccgcac gggaaaccgt tctcgccttt gtcagagaaa
     1261 actttgtcag tcagggcatg attgctgatg tggcgttcca tcacatggat aaaacaaatc
     1321 cccatgcgca catcatgctg accacgaggg ctatcggacc tgctgggttc agcggaaagg
     1381 tcagggactg gaacgaccgg acacatgccg agacgtggcg ggcatcatgg gctgaccatg
     1441 caaacagggc actggcgaac gccggttatc aggaagagat agaccatcgt tcatacgagc
     1501 gacaggggct tgagaaaacg cctggtattc acctcggaaa gtctgcctgt gcgatggaaa
     1561 cacgcggtat cgaaacagaa cgcggcgaac agaatcgtct gattaacagg cttaacctgg
     1621 aaatacagat ttcccgcacc gaactcagga acggagggct gacagagcct gcccgccgtg
     1681 tggctgacct tctgaatatc gggcttcctg acaacgcaac ttcgtacaca ctacgtgaca
     1741 ttatcgaagc gttgccgaag gacagtaact cggcatggaa actcaccagt aatgccatgt
     1801 cgatgatggc agatatgcag gcgacgcgca gacgctggga agagctgaac accgaacgaa
     1861 aggaagcgat gagccatgct gccagcctga aaaaatcatc gccgttttcg tccggttttt
     1921 cccgtattcc cctgatgcaa tgggcggcac cggaataccg tagtgagcag ggaaaaatcc
     1981 agtctctgag ccagcaaatg gaaaaattac gacagcatta ccggaaggtg gagaaacagg
     2041 acattcccgc gagtcagatg gcatttgaaa aacagtggca gcagtggggg gaatccggcc
     2101 ttgcagctct cagagcccag ttgcttaaac gtgaagagga attgcgccgg aaggaacagg
     2161 aagatactga acgtagtcgc gcggagcagc tcaggaaaaa tgacaatgcc gttatggatt
     2221 caggggtgct gagagcagtc gttacggggt atggcgaggc tcccatgcct ggtaacgggg
     2281 aaatgacctg ttaccttctg cttcacaacc ggaacggaga atatacgctc tgggggaacg
     2341 agctggagaa ataccgcacc agaatctttg agagtgttga tttaatgcgt gacaggagtg
     2401 gttatatctg tgaccgaagc gaaatcggcc aacgtccgcc actgcaacgt gtttattcct
     2461 ctgcaacctt tgagcaactg ctgacgcagg tttgccagac atggccgcaa catacccgca
     2521 atctccgcca gccgaagaca tggccggagt ctttctgtct tggagaagac cgccagccag
     2581 ccatgccatc accagcggca aggaaggtgg attttatgca gggacgtctg ccaccgacgc
     2641 tgatgccggt catgagttct gtcgaccggg aaacccgcca gcttcagctt ttgctggtca
     2701 tgggcgtgga tgactctctg ggcggtgtta tccggcttaa tggtacgctg tatcccgcgt
     2761 ttgccgttcc ctcagccgat aacaggcatc tggtcatcag tgcgctgacc gataaggggt
     2821 tacggtatgc agggtatggt gttgccgtaa atcacgatgc agacagccac atatcacctg
     2881 caccagaact gatgcagttt catctgaaaa cccgtgaggc accgcttttt gctgccgtca
     2941 acacaccaga aaaacagccg gatcatctgt tccgctcgct gggttttaat cgtacctggg
     3001 aggaatggca gcgcgaggaa gatgcacgaa cacacaccac cgagaggaga catgatcgcg
     3061 gttggtcaca gtgaatgtga acaatatttt gttttgttta acatcgtgtt atgttcgtcg
     3121 atgttcttcg atgttcatcg acagggatga atgcaagaag cacactcaca taacgcaagc
     3181 atagttttgt ttttccgccc ccaaaaattg gggggtcttt tttcgctgca tcagagcgtt
     3241 tttgacgcaa tttttcactt caatagtacc ttcgcactac taacacaaaa aaaacgcagc
     3301 agggagcgtt ttaggtgcct taaaatcgat tttagatcgt catcttgatc tgtttgtctt
     3361 ccttgaagcg aaaatgcagg gctacaaccg tgcgcccctt tttgatcgtc tcaacagtta
     3421 caaccagatc gcttttttcg ttcagttcgg cgatggctgg cttgattatc atcttattca
     3481 agtctttgaa ttgttgatat ttatcttcaa cggcaagcat ggttcggaaa tcatcgatag
     3541 ctatcgttct gtcaccggtg ctgcggaact gctggagcag ctcgtaaatg cggatgctgt
     3601 aggtgctgga aaggctggag acgttcttca cgactacccg cgtaaactgc cccttgagct
     3661 gtgtcagata cggcatgatg gcatcggaga aggtgatatc tactttcgcc tcacctttga
     3721 aatactgcgc ccggtactgc acccagcgga actcttctcg tttttcctcg ttcttgatga
     3781 ttactgacct gtcccagagg cgatctatcg cttccttgag cctagcttca gcgtgctgcc
     3841 gtcccatgtc aggaaaggca tcatgaaact ctgcagccgt gatggtcatg gttttttgtt
     3901 catccggcga aggggaatct tctccggatt tcaggcggct gatacagacc agcaggaagc
     3961 gctgttcctg caaagtgagc ttgtagcttg cctcgataag ggcgtttgat ttgtaagcta
     4021 tcagatctga catttcgctt gctcgttgct attggtggcg tttttttact gt
//
