LOCUS       NZ_CP051723             4072 bp    DNA     linear   CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-116 plasmid pSCU-116-4, complete
            sequence.
ACCESSION   NZ_CP051723
VERSION     NZ_CP051723.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14609778
            Assembly: GCF_012934555.1
KEYWORDS    RefSeq.
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 primary drivers of antibiotic resistance 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  JOURNAL   Unpublished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 (17-APR-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                   :: 21x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 01:49:14
            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)                     :: 5,046
            CDSs (total)                      :: 4,924
            Genes (coding)                    :: 4,721
            CDSs (with protein)               :: 4,721
            Genes (RNA)                       :: 122
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 94
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 203
            CDSs (without protein)            :: 203
            Pseudo Genes (ambiguous residues) :: 0 of 203
            Pseudo Genes (frameshifted)       :: 62 of 203
            Pseudo Genes (incomplete)         :: 141 of 203
            Pseudo Genes (internal stop)      :: 43 of 203
            Pseudo Genes (multiple problems)  :: 41 of 203
            Pseudo Genes (short protein)      :: 4 of 203
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP051723.1.
            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..4072
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-116"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-116-4"
                     /geo_loc_name="USA: California"
                     /collection_date="2015"
     gene            complement(<1..219)
                     /locus_tag="HHJ31_RS25065"
                     /pseudo=""
     CDS             complement(<1..219)
                     /locus_tag="HHJ31_RS25065"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001322464.1"
                     /note="incomplete; too short partial abutting assembly gap;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /name="hypothetical protein"
     gene            429..1121
                     /locus_tag="HHJ31_RS24965"
                     /old_locus_tag="HHJ31_24980"
     CDS             429..1121
                     /locus_tag="HHJ31_RS24965"
                     /old_locus_tag="HHJ31_24980"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001281399.1"
                     /GO_function="GO:0003887 - DNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /GO_process="GO:0006270 - DNA replication initiation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_001281403.1"
                     /translation="MSDLIAYKSNALVEASYKLTLQEQRFLLLCISRLKSGADAELQKT
                     MTITAAEYFDSFPDMGRKNAEVQLQEAIDRLWDRSIILKNDEKREEFRWIQYRAQYAKG
                     EAKARITFSDAVMPYLTQLKGQFTRVVIKNISGLSSSYSIRIYEFLQQFRSTGERIIAL
                     NDFRSMLGIENKYKQFRDLNKILIKPCVDELNKKSDLAVTVETIKKGRTVVALHFRFKE
                     DKQIKMTI"
                     /name="replication initiation protein"
     gene            complement(1377..3536)
                     /gene="mobQ"
                     /locus_tag="HHJ31_RS24970"
                     /old_locus_tag="HHJ31_24985"
     CDS             complement(1377..3536)
                     /gene="mobQ"
                     /locus_tag="HHJ31_RS24970"
                     /old_locus_tag="HHJ31_24985"
                     /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="MobQ family relaxase"
                     /protein_id="WP_001029353.1"
                     /translation="MAIYHLSMKIISRSSGYSAVASAAYRSGSLMLDERTGLTHDYTRK
                     SGVAEAVILTPATAPAWCTNRAELWNAVEKAECRKNSQLAREIELAIPRELPQDAARET
                     VLAFVRENFVSQGMIADVAFHHMDKTNPHAHIMLTTRAVGPAGFGGKVRDWNDRTHAET
                     WRASWADHANRALANAGYQEEIDHRSYERQGLEKTPGIHLGKSACAMETRGIETERGEQ
                     NRLINRLNLEIQISRTELRNSGLTEPARRVADLLNIVLPDNATSYTLRDIIEALPKDSN
                     AAWKLTSNAMSMMADMQATRRRWEELNTERKEAMSHAASLKKSSPFSSGFSRIPLMQWA
                     APEYRSEQGKIQSLSQQMEKLRQHYRKVEKQDIPASQTAFEKQWQQWGASGLAALRVQL
                     LKREEELRRKEQEDTERSRAERRAEQLRKNDNAVMDSGVLSAVVTGYGEAPMPGNGEMT
                     CYLLLHNRNGEYTLWGNELEKYRTRIFERVDLMRDRSGYICDRSEIGQHPPLQRVYSSA
                     TFEQLLTQVCQTWPQYTRNLRQPKTWPESFCLGEDRQPAMPSLAARKVDFTQGRLLPTL
                     MPVMSSVDRETRQLQLLLVMGVDDSLGGVVRLNGTLYPAFAVPSADNSQLVISALTDKG
                     LRYAGYGVAVNHDADSHISPAPELMEFHLKTREAPLFAAVNTPEKQPDHLFRSLGFNRT
                     WDEWRREEDARTHTTERRHDRGWSQ"
                     /name="mobQ"
     gene            3715..3969
                     /gene="mobC"
                     /locus_tag="HHJ31_RS24975"
                     /old_locus_tag="HHJ31_24990"
     CDS             3715..3969
                     /gene="mobC"
                     /locus_tag="HHJ31_RS24975"
                     /old_locus_tag="HHJ31_24990"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000091747.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase accessory protein MobC"
                     /protein_id="WP_000091747.1"
                     /translation="MSRTLEQKIADAEARLQRLKAKSRSLDTAQKVVVGAALLAKVRKP
                     EEVQLRAWLLQFLKAEVTRQADVTRILPLINELEALPGQ"
                     /name="mobC"
     Typing          complement(3179..3537)
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.056"
                     /coverage="100.0"
                     /evalue="3.94e-177"
     Typing          3538..3714
                     /name="MOBQ"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.876"
                     /coverage="100.0"
                     /evalue="1.22e-84"
     Typing          430..1121
                     /name="rep_cluster_1778"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.965"
                     /coverage="100.0"
                     /evalue="0.0"
     Typing          complement(1381..3623)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.332"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttttcggtag gtgatatgcg ctgaacccgc atgaatactg gatttccaca gggttggaag
       61 gggagtattc ggaacttgca attctgcttt cttgcaacac attgttttta ttggtttttt
      121 gttttcagcg ccccgagtta tccacaggct cgccgttaag tttttagatc ttgtttttaa
      181 gatcttgttt ttaatacttg ttttagggtc aaaattcatt aataaaatca atatgttata
      241 gaggtatatg tggaggaatt taaggtaaag gtggaggaat ttaaggtgtt taggtggagg
      301 aatttaaggt aaaggtggag gaatttaagg tgttattcac agaaatgtga ggatataaaa
      361 aaaaatattc cacatttctt atttgtgggg cacattaaag catcaccaca tttgaacggg
      421 atctttgtat gtcggacttg attgcctaca agtcgaatgc tttggttgag gccagctaca
      481 agttgaccct acaggaacaa cgttttctgt tgctgtgtat cagtcgattg aaatctggtg
      541 ctgatgctga attgcaaaag acaatgacca ttaccgctgc ggaatatttt gattcattcc
      601 ctgacatggg gcggaaaaat gccgaggttc agttacagga agcgatcgat cgtttatggg
      661 acaggtcgat cattctcaag aatgacgaga agcgtgagga gttccgctgg atccagtatc
      721 gggcacagta cgctaaaggt gaggccaagg ctcgaataac cttttctgac gcggtaatgc
      781 cttatctgac gcaactgaag gggcaattca cgcgcgttgt tataaaaaac atatcaggtt
      841 tatcaagtag ttacagtata agaatatacg agttcctcca gcaattccgc agtacgggag
      901 agagaattat tgctcttaat gactttcgtt caatgttagg gattgaaaat aaatacaaac
      961 aattcagaga cttaaataaa atactaataa aaccctgtgt tgacgaactg aacaaaaaaa
     1021 gcgacctggc tgtaacggtt gagacgatca aaaaggggcg cacggttgta gccctgcatt
     1081 ttcgcttcaa ggaagacaaa cagatcaaga tgacgatcta aaatcgattt taaggcacct
     1141 aaaacgctcc ctgctgcgtt ttttttgtgt tagtagtgcg aaggtactat tgaagtgaaa
     1201 aattgcgtca aaagcgctct aatgcagcga aaaaagaacc cccaattttt gggggcggaa
     1261 aaacaaaact atgcttgcat tatgtgtgtg cttcttgcat tcatccctgt cgatgaacat
     1321 agaagaacat cgacgaacat aacacgatgt taaacaaaac aaaatattgt tcacattcac
     1381 tgtgaccaac cgcgatcatg tctcctctcg gtggtgtgtg ttcttgcatc ttcctcgcgc
     1441 cgccattcat cccaggtacg attgaaaccc agagagcgga acagatgatc cggctgtttt
     1501 tctggtgtgt tgacggcagc aaaaagcggt gcctcacggg ttttcagatg aaactccata
     1561 agttccggcg caggtgatat gtggctgtct gcatcgtgat ttacggcaac accataccct
     1621 gcataccgta accccttatc ggtcagtgca ctgatgacca gctggctgtt atcggctgag
     1681 ggaacggcaa acgcgggata cagcgtacca ttaagccgga caacaccgcc cagagagtca
     1741 tccacgccca tgaccagcaa aagctgaagc tggcgggttt cccggtcgac agaactcatt
     1801 accggcatca gcgtcggtag cagacgtccc tgcgtaaaat ccaccttcct tgctgccagt
     1861 gatggcatgg ctggctggcg gtcttctcca agacagaaag actccggcca tgtcttcggc
     1921 tggcggagat tgcgggtata ttgcggccat gtctggcaaa cctgcgtcag aagttgctca
     1981 aaggtcgcag aggaataaac acgttgcagt ggtggatgtt gaccgatttc gcttcggtca
     2041 cagatataac cactcctgtc acgcattaaa tcaacacgct caaagattct ggtgcggtat
     2101 ttctccagct cgttccccca gagcgtgtat tctccgttcc ggttgtgaag cagaaggtaa
     2161 caggtcattt ccccgttacc aggcatgggg gcctcgccat accccgtaac gactgcgctc
     2221 agtacccctg aatccataac ggcattgtca tttttcctga gctgttccgc tcgtcgctcc
     2281 gcgcgactac gttctgtatc ctcctgctcc ttccggcgca attcctcttc acgtttaagc
     2341 aactggactc tgagagctgc aaggccggat gccccccact gctgccactg tttttcaaat
     2401 gccgtctgac tcgcgggaat gtcctgtttc tccaccttcc ggtaatgctg tcgcaatttt
     2461 tccatttgct ggctcagcga ctggattttt ccctgttcgc tacggtattc cggtgccgcc
     2521 cattgcatca ggggaatacg ggaaaaaccg gacgaaaacg gcgatgattt tttcaggctg
     2581 gcagcatggc tcatcgcttc ctttcgttcg gtgttcagct cttcccagcg tctgcgcgtc
     2641 gcctgcatat ctgccatcat cgacatggca ttactggtga gtttccatgc cgcattactg
     2701 tccttcggca acgcttcgat gatgtcacgt agtgtgtacg aagttgcgtt gtcaggaagc
     2761 acgatattca gaaggtcagc cacacggcgg gcaggctctg tcagcccgct gttcctgagt
     2821 tcagtgcggg aaatctgtat ttccaggtta agcctgttaa tcagacgatt ctgttcgccg
     2881 cgttctgttt cgataccgcg tgtttccatc gcacaggcag actttccgag gtgaatacca
     2941 ggcgttttct caagcccctg tcgctcgtat gaacgatggt ctatctcttc ctgataaccg
     3001 gcgttcgcca gtgctctgtt tgcatggtca gcccatgatg cacgccacgt ctcggcatgt
     3061 gtccggtcgt tccagtccct gacctttccg ccgaacccag caggtccgac agccctcgtg
     3121 gtcagcatga tgtgcgcatg gggatttgtt ttatccatgt gatggaacgc cacatcagca
     3181 atcatgccct gactgacaaa gttttctctg acaaaggcga gaacggtttc ccgtgcggca
     3241 tcctgcggca gttcacgggg gatagcgagt tcaatttccc gcgcaagttg tgagttcttc
     3301 cggcattcgg ccttctcaac ggcattccag agttcggcac ggttcgtaca ccaggcaggg
     3361 gctgtcgcgg gggtcagaat cacagcttca gccacaccgc ttttgcgggt gtagtcgtga
     3421 gtcagtccgg tacgctcatc aagcatcagt gaaccggaac gataggcagc ggaagctacg
     3481 gcgctgtagc cgctgcttct ggagataatt ttcatgctga gatgataaat cgccatttct
     3541 gccgtaatgc ctttttgtag ttttctttca gccccgcagg gcgcacacaa tcgaaacgga
     3601 gtggagattg tataagtgcg caatttgtga tttgtcgtgc attatgccag ctcagttttt
     3661 aaactaccag tgacgcgcta aaatgcgatt tttcatcgcg cacggagtta catcatgagc
     3721 agaacgctcg aacagaagat tgctgatgct gaggcgagat tacagcgcct gaaggcgaag
     3781 agccggagcc tggacacagc gcagaaggtt gttgtgggtg cagcattgct ggcaaaggtc
     3841 agaaagccgg aggaggtgca gttgcgtgcc tggttactcc agttcctgaa ggcagaggtg
     3901 acacgacagg ctgatgtgac gcgcatactg ccgctgatta acgagctgga ggcgctgcca
     3961 ggacagtgat tgtatcgtcc gctcgccgca gccccagcga ccgagcgtta gcgagcgagt
     4021 gggcgaggaa gcggaagtga atccgtcgcc aggttgagca catacgcacg gt
//
