LOCUS       NZ_CP051747             6320 bp    DNA     circular CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-484 plasmid pSCU-484-3, complete
            sequence.
ACCESSION   NZ_CP051747
VERSION     NZ_CP051747.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14609800
            Assembly: GCF_012934785.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 6320)
  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  JOURNAL   Unpublished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 6320)
  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                   :: 38x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 02:28:45
            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)                     :: 5,085
            CDSs (total)                      :: 4,969
            Genes (coding)                    :: 4,723
            CDSs (with protein)               :: 4,723
            Genes (RNA)                       :: 116
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 88
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 246
            CDSs (without protein)            :: 246
            Pseudo Genes (ambiguous residues) :: 0 of 246
            Pseudo Genes (frameshifted)       :: 148 of 246
            Pseudo Genes (incomplete)         :: 121 of 246
            Pseudo Genes (internal stop)      :: 52 of 246
            Pseudo Genes (multiple problems)  :: 61 of 246
            Pseudo Genes (short protein)      :: 3 of 246
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP051747.1.
            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..6320
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-484"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-484-3"
                     /geo_loc_name="USA: California"
                     /collection_date="2018"
     gene            complement(join(6300..6320,1..213))
                     /locus_tag="HHJ53_RS25085"
                     /old_locus_tag="HHJ53_25095"
     CDS             complement(join(6300..6320,1..213))
                     /locus_tag="HHJ53_RS25085"
                     /old_locus_tag="HHJ53_25095"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137438.1"
                     /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="WP_011117658.1"
                     /translation="MTELETHLLNALEQLQQDYMQRLSEWESAFVELQKMFSRTQRDNA
                     MLNERVMQLSQQVQHLSEQTERLSQLYSENWR"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(220..738)
                     /locus_tag="HHJ53_RS25090"
                     /old_locus_tag="HHJ53_25100"
     CDS             complement(220..738)
                     /locus_tag="HHJ53_RS25090"
                     /old_locus_tag="HHJ53_25100"
                     /inference="COORDINATES: protein motif:HMM:NF016710.2"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_015328227.1"
                     /translation="MSNLLQTGAEFEKKLKERAESTEKMLNDEFRKLGESVSEAVTSNE
                     TKIRDAIALFTASTEKSLEKHREGVKEAMMQHRKDVLKLAGNTGMMLLGIVFLLFTASG
                     GTLWYLGGRIQANLEEIRKQEETLQKLNAKTWGVEFVQDGNRKFLVLPYGKSAEVIPFQ
                     GKEWVHLKE"
                     /name="MbeB family mobilization protein"
     gene            complement(<776..1207)
                     /locus_tag="HHJ53_RS25880"
                     /old_locus_tag="HHJ53_25105"
                     /pseudo=""
     CDS             complement(<776..1207)
                     /locus_tag="HHJ53_RS25880"
                     /old_locus_tag="HHJ53_25105"
                     /inference="COORDINATES: protein motif:HMM:NF015397.2"
                     /note="incomplete; partial in the middle of a contig;
                     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            complement(1416..1739)
                     /locus_tag="HHJ53_RS25100"
                     /old_locus_tag="HHJ53_25110"
     CDS             complement(1416..1739)
                     /locus_tag="HHJ53_RS25100"
                     /old_locus_tag="HHJ53_25110"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_069354221.1"
                     /translation="MLTIRVTDDEHARLLERCEGKQLAVWMRRVCLGEPVARSGKLPTL
                     APPLLRQLAAIGNNLNQTARKVNSGQWSSCDRVQVVAALMAIERELRSLRQVVREQGAR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1804..1995
                     /locus_tag="HHJ53_RS25105"
                     /old_locus_tag="HHJ53_25115"
     CDS             1804..1995
                     /locus_tag="HHJ53_RS25105"
                     /old_locus_tag="HHJ53_25115"
                     /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="WP_000165985.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNELDADEQADICESLHDHA
                     DELYRSCLARFGDDGENL"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(3088..3984)
                     /locus_tag="HHJ53_RS25110"
                     /old_locus_tag="HHJ53_25120"
     CDS             complement(3088..3984)
                     /locus_tag="HHJ53_RS25110"
                     /old_locus_tag="HHJ53_25120"
                     /EC_number="2.1.1.72"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011117660.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Dam family site-specific
                     DNA-(adenine-N6)-methyltransferase"
                     /protein_id="WP_001570854.1"
                     /translation="MKDKVFVPPIKSQGIKTKLVPWIKRIVPKNFNGVWVEPFMGTGVV
                     AFNVAPKDALLCDTNPHLISFYNALKNKDITGDLVKDFLYREGEKLLLSNGEYYYEVRE
                     RFNNYKEPLDFLFLNRSCFNGMIRFNSKGGFNVPFCKKPNRFAQAYITKISNQVDRISE
                     IISKGNYTFLCQSFEKTIGMVNRDDVVYCDPPYIGRHVDYFNSWGERDERLLFETLSSL
                     NATFITSTWHHNDYRENKYVRDLWSSFRILTKEHFYHVGASEKNRSPMVEALITNIAKD
                     IIDHIEKSSGDILVIEE"
                     /name="Dam family site-specific
                     DNA-(adenine-N6)-methyltransferase"
     gene            4008..4307
                     /locus_tag="HHJ53_RS25115"
                     /old_locus_tag="HHJ53_25125"
     CDS             4008..4307
                     /locus_tag="HHJ53_RS25115"
                     /old_locus_tag="HHJ53_25125"
                     /inference="COORDINATES: protein motif:HMM:NF024252.2"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix transcriptional regulator"
                     /protein_id="WP_015328228.1"
                     /translation="MPKKPILGYPILGCIIYKKNDGKSMSVREIIKKNRVICKLSQGEV
                     AKALGKPQSYISKIEQGERRVDVDEFIAICFAIGIDPINTLKEVIMEKKHESSF"
                     /name="helix-turn-helix transcriptional regulator"
     gene            4291..5028
                     /locus_tag="HHJ53_RS25120"
                     /old_locus_tag="HHJ53_25130"
     CDS             4291..5028
                     /locus_tag="HHJ53_RS25120"
                     /old_locus_tag="HHJ53_25130"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013934312.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type-2 restriction enzyme EcoRV"
                     /protein_id="WP_011117659.1"
                     /translation="MSLRSDLINALYDENQKYDVCGIISAEGKIYPLGSDTKVLSTIFE
                     LFSRPIINKIAEKHGYIVEEPKQQNHYPDFTLYKPSEPNKKIAIDIKTTYTNKENEKIK
                     FTLGGYTSFIRNNTKNIVYPFDQYIAHWIIGYVYTRVATRKSSLKTYNINELNEIPKPY
                     KGVKVFLQDKWVIAGDLAGSGNTTNIGSIHAHYKDFVEGKGIFDSEDEFLDYWRNYERT
                     SQLRNDKYNNISEYRNWIYRGRK"
                     /name="type-2 restriction enzyme EcoRV"
     Typing          complement(2107..2194)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="6.86e-39"
     Typing          2218..2762
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="95.446"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          complement(9..1426)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="96.406"
                     /coverage="90.0"
                     /evalue="0.0"
ORIGIN
        1 taactggctc aagcgttctg tctgctcgct caagtgctgc acctgctgac tcaactgcat
       61 gacccgctcg ttcagcatcg cgttgtcccg ttgcgtacgc gaaaacatct tctgcaattc
      121 cacgaaggcg ctctcccatt cgctcagccg ctgcatatag tcctgttgca gctgctctaa
      181 ggcgttcagc aaatgtgttt ccagctctgt cattctgtgt cactccttca gatgtaccca
      241 ctctttcccc tgaaagggaa tcacctctgc tgatttcccg tacggaagga ccagaaattt
      301 cctgttcccg tcctgcacaa actccacgcc ccatgtcttc gcgttcagtt tctgcaatgt
      361 ctcttcctgc ttcctgattt cttccaggtt cgcctgtatc ctcccgccaa gataccagag
      421 cgtcccgcca ctcgcggtaa acaggagaaa gactatcccc agtaacatca tgcccgtatt
      481 ccctgccagc tttaacacgt ccttcctgtg ctgcatcatc gcctctttca ccccttccct
      541 gtgtttttcc agcgatttct ctgtcgaggc tgtgaacagg gctatagcgt ctctgatttt
      601 cgtctcgttt gaggtcacag cctcgctgac agactcgccg agcttcctga actcgtcgtt
      661 cagcattttc tctgtagatt cggctctctc tttcagcttt ttctcgaact ccgcgcccgt
      721 ctgtaaaaga ttgctcataa aacgctcctt tcagcctgat attcttcccg ccgttcgggt
      781 ctgcaatgct gatgctgctt cgcgtcaccc tgaccacttc aagccccgcc tctgtgagcg
      841 cctgaatcac atcctgacgg ccttttatct cccctacatg ataaagagcg tctatcccgc
      901 gtgtgacgct ctcagcaagc gcctgtttcg tttccggcag gttatcagag agagtcagta
      961 tccggcggtt ctccggggcg ttggggtcat gcagcccgta atggtgattc accagcgtct
     1021 gccaggcatc aattctcggc ctgtctgccc ggtcgtagta cggctggaga cgttttccgg
     1081 tctgtagctc catgttcgga atgataaaat tcagctcaag ccgtcccttg tcctggtgct
     1141 ccacccacag gatgctgtac tgattctttt cgagacctgg catcagtacg cgctcaaagc
     1201 tcgccatcac tttttcacgt cctcccggcg gcagttcctt ctccgcgaac gacagaacac
     1261 cggacgtgta tttcttcgca aatggcgtgg catcgatgag ttcccggact tcttccggat
     1321 taccctgaag caccgttgcc ccttcccggt tacgctccct ccccagcagg taatcaaccg
     1381 gaccactgcc accacctttt cccctggcat gaaatttaac tatcatcccg cgccccctgt
     1441 tccctgacga cctgccgtaa gctgcgcaac tctctctcga tggccatcag tgcggccacc
     1501 acctgaaccc ggtcacagga agaccactgc ccgctgttca ccttcctcgc cgtctgattc
     1561 aggttattcc cgatggcagc cagctggcgc agtaacggcg gtgccagtgt cggcagcttc
     1621 ccggaacggg caaccggctc acccaggcag acccgccgca tccataccgc cagctgttta
     1681 ccctcacagc gttccagtaa ccgtgcatgt tcatcatcag taacccgtat cgtgagcatc
     1741 ctctcgcgtt tcatcggtat cattacccca tgaacagaaa tcccccctta cacggaggca
     1801 tcagtgacta aacaggaaaa aaccgccctt aacatggccc gctttatcag aagccagaca
     1861 ttaacgctgc tggagaagct caacgaactg gacgcagatg aacaggcaga catctgtgaa
     1921 tcgcttcacg accacgccga tgagctttac cgcagctgcc tcgcacgttt cggggatgac
     1981 ggtgaaaacc tctgacacat gcaactcccg gagacgctca cagcttgtct gctcccggag
     2041 acgctcacag cttgtctgtg agcgtctccg ggagcagaca agcccgtcag ggcgcgtcag
     2101 caggttttag cgggtgtcgg ggcgcagccc tgacccagtc acgtagcgat agcggagtgt
     2161 atactggctt aaccatgcgg catcagtgcg gattgtatga aaagtacgcc atgccgggtg
     2221 tgaaatgccg cacagatgcg taaggagaaa atgcacgtcc aggcgctctt ccgcttcctc
     2281 gctcactgac tcgctacgct cggtcgttcg actgcggcga gcggtgtcag cgcactcaaa
     2341 ggcggtaaac ggttatccac agaatcaggg gataacgccg gaaagaacat gtgagcaaaa
     2401 gacaaagacc cagaaaaagg gcgcgcagga ggcgtttttc cataggctcc gcccccctga
     2461 cgagcatcac aaaaatcgac gctcaagtca gaggtggcga aacccgacag gactataaag
     2521 ataccaggcg tttccccctg gaagctccct cgtgcgctct cctgttccga ccctgccgct
     2581 taccggatac ctgtccgcct ttctcccttc gggaagcgtg gcgctttctc atagctcacg
     2641 ctgttggtat ctcagttcgg tgtaggtcgt tcgctccaag ctgggctgtg tgcacgaacc
     2701 ccccgttcag cccgaccgct gcgccttatc cggtaactat cgtcttgagt ccaacccggt
     2761 aagacacgcc ttaacgccac tggcagcagc cactggtaga ggatgtacaa gaaattgctg
     2821 atacgtagtt cttgaagtga aggaccaact gcggctacac tgaaaggaca gatttggtgg
     2881 cagcggtctt gtacaccctg ttaccacggt taaataatct gccaggatta tttaaccttc
     2941 gaaaaaccac ctgccagggt ggttttttcg tctacagaca gcagattacg cgcgaaaaaa
     3001 aaggatctca agaggatctt gagatctttt tacatatccc ctctcacgat aaacgtacag
     3061 agtggtcact ttatgtcctc atctccatca ctcttcaatt accaaaatat ccccactact
     3121 tttttcaatg tgatcaataa tatccttggc tatatttgta attagcgcct ctaccatcgg
     3181 ggatctgttt ttttcggacg ctccaacatg ataaaaatgt tcttttgtca atattctaaa
     3241 agatgaccat aaatcacgaa cgtacttatt ttccctataa tcattatgat gccacgtaga
     3301 cgttataaat gtagcattca aagatgataa cgtttcaaat aataaacgct cgtcacgctc
     3361 tccccatgaa ttaaaataat caacatgcct accaatatat ggaggatcac aataaacaac
     3421 atcatcccta tttaccatgc caatagtttt ttcaaatgac tgacacaaga atgtatagtt
     3481 cccttttgat attatttcag aaatcctatc aacttgattc gaaatcttgg taatatatgc
     3541 ttgtgcaaat ctgtttggtt ttttacaaaa aggaacatta aaccctcctt tactattaaa
     3601 cctaatcata ccattaaaac aagacctatt taagaataaa aaatctaacg gttccttgta
     3661 attattaaac ctttccctga cttcataata atactcacca ttacttaata agagtttttc
     3721 accttcacga tataaaaaat ccttaacaag atcccctgtt atatctttat ttttcaatgc
     3781 attataaaaa gaaatcaaat gagggtttgt atcacataat aatgcatctt taggagcaac
     3841 gttaaaggca acaactccag tccccataaa cggctcgacc cataccccat taaagttttt
     3901 aggaacaatt ctctttatcc acggaaccag tttagtctta atcccttgcg attttatagg
     3961 cggaacaaaa actttatctt tcataataag aaccatttgt aaaaaatatg ccaaagaaac
     4021 ccattttggg ttatcccatt ttggggtgca taatatataa aaaaaatgat ggtaaatcta
     4081 tgtctgtaag agaaatcata aaaaaaaata gagtaatttg taaactctct caaggagagg
     4141 ttgccaaggc acttggaaag ccacaatcct acatatctaa aatagaacaa ggagaaagac
     4201 gcgttgacgt tgacgaattt atagccatct gttttgcaat aggaattgac ccaataaata
     4261 cacttaaaga agtaataatg gaaaaaaaac atgagtcttc gttctgattt aattaatgca
     4321 ctatatgatg aaaatcaaaa atatgatgta tgcggaataa tatctgcaga aggaaaaata
     4381 tacccattgg gaagtgacac aaaagttcta agcacaatat ttgagttatt ctcaagacca
     4441 ataataaata aaatagcaga aaaacatggg tatattgtag aagaacctaa acaacaaaat
     4501 cattatcctg actttactct ttacaaacca agcgaaccaa ataaaaaaat tgcaatagat
     4561 ataaaaacaa catatacaaa caaagaaaac gaaaaaatca agttcactct tggtgggtat
     4621 accagcttta tacgaaacaa cacaaaaaat attgtttatc catttgacca atatatcgcc
     4681 cattggataa tcggatatgt atatacaaga gttgctacaa gaaaatcatc tttaaaaaca
     4741 tataatataa atgaactcaa tgaaatccct aaaccataca aaggcgtaaa ggttttctta
     4801 caagataaat gggttattgc tggagatttg gcaggatctg gaaacacaac aaatataggt
     4861 agcattcatg cccactataa agactttgta gaaggaaaag gaatatttga ctcagaggat
     4921 gagtttttag actattggag aaattatgaa agaaccagtc aattaagaaa tgacaagtat
     4981 aataatataa gcgaatacag aaactggata taccgaggaa gaaaataagc aatagcttat
     5041 atgtttatat cccccccctc taacagagaa taaaacctct ctgactcatg agagaaagag
     5101 ggggagggag ggatactaaa agaaaaaatt tagcatcaga ctattccctc ctccggcaca
     5161 tcacacttaa cattcaaaga tgacatgatg cacccttaca ctctcaccac aacaacataa
     5221 agacataaaa acatatgcct ctctatattt tccctctgca tttcgcacaa taaatataca
     5281 tatcacttga atgatgttta attcaacacc aatgagagag aattttttct gtatgtctat
     5341 acattgcgga aaataagaat tgggtgcgct tctcacattg agaccggtta caatgataaa
     5401 cgactagaaa cgcacccatg tccgttgtaa cttgattctt aataaaaatc aacacatttt
     5461 tgttaattac aaaaagtatt tttagcttat cataaaccac acgcatattt ttatataaac
     5521 agcttctttt attgcaacga acacaataat aaaataaaat agaaaaccat tatatgtaat
     5581 ataatgacgt ttatttactt cttgttattc atacacctct ttacataaac gcgcccttac
     5641 aaaaaatcaa tacatcagtt gaggaaattt cttgatatag tttaatatta gaatcactgg
     5701 catcagtcct catgtattct tatttacaac atcacttctc ctccgactct tagagagttt
     5761 agtatttaaa taatgtataa tttaaaaccc caatacagga taagcattaa atgctatata
     5821 tcaacagcat tgcctatcaa atcacatact ctaaaagtaa atcatatcct cgtcttttat
     5881 tgtaataaaa gaaatttatt aataatgcat cgagatggaa aataaatgat aaatagcttt
     5941 atagtcaaat ataagccata ggcccccacc ctgagcttat ctattatatt taacataatt
     6001 acaaattgta cgcaccgcca aaacgcgttc agcgcgatca cagcagcaga caggtaaaaa
     6061 tggcaacaaa ccacccgaaa aactgccgca atcgcgcctg ataaatttta accgcatgaa
     6121 tacctatgca accagatggt acagaccaca ttagcctgtc ttaatccact taacctgcca
     6181 tttttcatag tttcaccatc ccagcgaagg accatccagt gtgcgttcct gtatttccag
     6241 ctggcgctca cgctccaggg ataacgcatg ttcgcgctcc tgtatcagtc gttcctctct
     6301 tatctccagt tctcgctgta
//
