LOCUS       NZ_CP054351             3896 bp    DNA     circular CON 13-JUN-2023
DEFINITION  Escherichia coli strain SCU-176 plasmid pSCU-176-6, complete
            sequence.
ACCESSION   NZ_CP054351
VERSION     NZ_CP054351.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14943547
            Assembly: GCF_013315675.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 3896)
  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  JOURNAL   Unpublished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 3896)
  AUTHORS   Stephens,C., Arismendi,T., Wright,M., Hartman,A., Gonzalez,A.,
            Gill,M., Pandori,M. and Hess,D.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-MAY-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                   :: 100x
            Sequencing Technology :: Illumina MiSeq, Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 06/13/2023 03:58:56
            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)                     :: 4,962
            CDSs (total)                      :: 4,848
            Genes (coding)                    :: 4,620
            CDSs (with protein)               :: 4,620
            Genes (RNA)                       :: 114
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 6
            Pseudo Genes (total)              :: 228
            CDSs (without protein)            :: 228
            Pseudo Genes (ambiguous residues) :: 0 of 228
            Pseudo Genes (frameshifted)       :: 88 of 228
            Pseudo Genes (incomplete)         :: 149 of 228
            Pseudo Genes (internal stop)      :: 51 of 228
            Pseudo Genes (multiple problems)  :: 52 of 228
            Pseudo Genes (short protein)      :: 3 of 228
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP054351.1.
            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..3896
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="SCU-176"
                     /isolation_source="rectal swab from healthy college
                     student"
                     /host="Homo sapiens"
                     /db_xref="taxon:562"
                     /plasmid="pSCU-176-6"
                     /geo_loc_name="USA: California"
                     /collection_date="2017"
     gene            complement(1166..2314)
                     /locus_tag="HPE52_RS24550"
                     /old_locus_tag="HPE52_24540"
     CDS             complement(1166..2314)
                     /locus_tag="HPE52_RS24550"
                     /old_locus_tag="HPE52_24540"
                     /EC_number="2.1.1.37"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003801590.1"
                     /GO_function="GO:0003886 - DNA
                     (cytosine-5-)-methyltransferase activity [Evidence IEA];
                     GO:0008168 - methyltransferase activity [Evidence IEA];
                     GO:1904047 - S-adenosyl-L-methionine binding [Evidence
                     IEA]"
                     /GO_process="GO:0006304 - DNA modification [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DNA cytosine methyltransferase"
                     /protein_id="WP_001529706.1"
                     /translation="MRSLEIFSGAGGLAKGLELAGFQHVGFVELNKHACDSLRLNFDEE
                     KVFQGDIKNYDLSSLDKIDIVAGGPPCQPFSLGGKHKAHDDSRDMFPFAIKAIEVLQPK
                     AFIFENVKGLLRKSFADYFEYIILRLTYPCLSLSNVSDWRIHLDVLRKARKDKHCGCTY
                     DVSFKLINAADYGVPQIRERVIIVGVRSDLNKKWSFPSVTHTQEKLLWEQHVTGDYWRK
                     HNIDAVIDKGISERLMKRFGIFPPSGKSWVTVRDALKNVPQPYESHGIGDHIFKDGARV
                     YPGHTGSYIDLPSKTLKAGAHGVPGGENMIRYEDGTVRYFTVYEGKLLQTFPREFLIAG
                     AWGEAMRQIGNAVPVLLAQKIGQQLYNLLNEEVEPLLCSNFN"
                     /name="DNA cytosine methyltransferase"
     gene            complement(2314..2958)
                     /locus_tag="HPE52_RS24555"
                     /old_locus_tag="HPE52_24545"
     CDS             complement(2314..2958)
                     /locus_tag="HPE52_RS24555"
                     /old_locus_tag="HPE52_24545"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001529705.1"
                     /GO_function="GO:0004518 - nuclease activity [Evidence
                     IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Eco29kI family restriction endonuclease"
                     /protein_id="WP_001529705.1"
                     /translation="MHNKKFDRSEHVYRNDSFLELIKDAVRFFSGTPVHSLPPPERFQG
                     AGVYALYYTGHYSLYDEYSRINRLAYNLPIYVGKAVPAGWRQSRISDHETRAGSELSNR
                     IREHGRNIAKTSNLDLCDFSCRFVIFEATGSDMISTVEAALIKIYKPLWNTVVDGFGNH
                     TPGAGRFAQAKSDWDVIHPGREWAEKCTGVHSEPYFIEERIKQYFSKSNFT"
                     /name="Eco29kI family restriction endonuclease"
     Typing          complement(192..276)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.837"
                     /coverage="100.0"
                     /evalue="1.41e-35"
     Typing          296..844
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.595"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 catcctgccc cgtcctgtac gtgttttttt caccagaaca acttcacgaa gtggcggatg
       61 aacgctacca acgttgccgg gaacgcttcg gcgatgatgg cataacgggc tgatacaggc
      121 agctcccgga gacggtcaca gcttgcctgt gagcggatgc cgggagccga caagcccgtc
      181 agggcgcgtc agggggtttc ggggcgaagc cctgaaccag tcacgtagcg atagcggagt
      241 gtatactggc ttaaccatgc ggcatcagtg cagattgtaa gaaaagagca ccatatgcgg
      301 tgtgaaatgc cgcacagatg cgtaaggaga aaatgcacgt tccggcgctc ttccgcttcc
      361 tcgctcactg actcgctgcg ctcggtcgtt cggctgcggc gagcggtgtc ggctcactca
      421 aaagcggaga tgcggttatc cacagaatca ggggataacg ccaaaagaaa catgtgagca
      481 aaaaacgaga acccggaaaa ggccacgccg ctggcgtttt tccataggct ccgcccccct
      541 gacgagcatc acaaaaatcg acgctcaagt cagaggtggc gaaacccgac aggactataa
      601 agataccagg cgtttccccc tggaagctcc ctcgtgcgct ctcctgttcc gaccctgccg
      661 cttaccggat acctctccgc ctttctccct tcgggaagcg tggcgctttc tcatagctca
      721 cgctgttggt atctcagttc ggtgtaggtc gttcgctcca agctgggctg tgtgcacgaa
      781 ccccccgttc agcccgaccg ctgcgcctta tccggtaact atcgtcttga gtccaacccg
      841 gtaagacacg ccttaacgcc actggcagca gccattggta actggacaag gtggattgag
      901 atattaagag ttcttgaagt ggtggcctaa ctgaggctac actagaagga cagtatttgg
      961 tatctgcgct ccaccaagcc agttaccttc gggaaaaaga gttggtagct cttgattccg
     1021 gcaaacgaac caccgttggt agcggtggtt tttttgttta caggcagcag attacgcgca
     1081 gaaaaaaagg atctcaagaa gatcctttga tctttttttg caaattgcct ctatggctgt
     1141 atcaccacca tagagacaca aacttttaat tgaagttaga gcacaataac ggctcaacct
     1201 cttcattcaa taagttatac aattgctgcc ctatcttctg agctagcaac acaggaactg
     1261 cattaccaat ctgcctcata gcctcccccc aagctcctgc aatcagaaac tctcgaggaa
     1321 aagtctgaag aagcttccct tcataaaccg taaaataacg aacagtccca tcctcatacc
     1381 taatcatatt ttcacctcca ggtacgccat gagcgccagc cttaagtgtt tttgaaggca
     1441 aatcgatata acttccagta tgaccaggat aaactcgagc gccatcttta aagatatgat
     1501 ctccaatacc atgtgactca tacggttgag gaacattctt taatgcgtcc ctaacagtaa
     1561 cccagctttt ccccgatggg gggaaaatac caaaacgttt cattaaacgc tcagaaatac
     1621 ctttatctat aaccgcatca atattatgct ttcgccaata gtcaccagta acatgctgtt
     1681 cccacagcaa tttttcttga gtatgcgtta cacttggaaa agaccatttt ttattcaaat
     1741 cacttcgaac accaacaatt atgacccgtt ccctaatttg tggaactcca taatcagctg
     1801 cattgattaa tttaaaactg acatcatatg tacacccaca gtgtttatcc ttgcgagctt
     1861 ttcttaatac atctagatgt attctccaat cacttacatt acttaacgat aaacaaggat
     1921 aagtcaaacg aagaattatg tattcaaaat agtccgcaaa tgattttcta agcaaccctt
     1981 taacattttc aaaaataaaa gcttttggtt gcaatacttc aattgctttt attgcaaatg
     2041 gaaacatatc cctagagtca tcatgagctt tatgttttcc gcccaatgaa aatggttggc
     2101 aaggaggccc gccagcaaca atatctattt tatctagaga tgaaaggtca taatttttaa
     2161 tatctccctg aaataccttc tcctcatcaa aattaagtcg caaagaatca catgcatgct
     2221 tgtttaactc aacaaatcct acatgctgaa atcctgccaa ctctagacct ttagccaagc
     2281 cgccggctcc tgaaaaaatc tctaatgatc tcattatgta aaattactct tagaaaaata
     2341 ctgtttaatt ctctcctcaa taaagtatgg ctcagaatga acacctgtac atttctcagc
     2401 ccactccctg ccaggatgta ttacatccca atcagattta gcttgcgcaa atcgcccggc
     2461 accaggggta tgatttccaa agccatcaac aacggtattc cacaaaggct tataaatttt
     2521 aataagagcg gcctcaactg tactaatcat atcagacccc gtagcctcaa agataacaaa
     2581 gcgacatgaa aaatcacaca aatctagatt cgatgttttt gctatatttc ggccatgttc
     2641 tctaattcta ttagatagtt cagaaccagc cctagtttca tgatcactaa ttctagactg
     2701 acgccaacca gcaggaacag ccttgccaac ataaatagga aggttatatg ccaacctatt
     2761 tatacgagaa tattcatcat ataatgaata atgtcctgta tagtaaagag catacacccc
     2821 agcaccttga aaccgttccg gtggtggtaa tgaatgaaca ggcgtaccac taaaaaaacg
     2881 aacggcatct tttattaact ctaggaaaga gtcatttcta taaacatgct cagatctatc
     2941 aaatttctta ttgtgcatta tgttttccga aaggtcttta tattaacact cctactcaac
     3001 atcacctatg atacgatcat aaagctaata ccccaaccca tacgcattta ccataacgtc
     3061 gcattgtacg caccgttaaa acgcgctcag cgcgcttctg gcgcaaaaac cgtaaaaatg
     3121 gatgttttcc cccgggtaaa ccggaaaaat gcgtcaggaa cgctttcagc gcgttgcatg
     3181 actatgcata aaactgaatg gcgagcggtt tgggcgcgtc tgatgcccat aaggcgtatt
     3241 ttctgacgtt ttcagccctg ataagaagaa atcagactgt agttacagac gagtcgtgag
     3301 cgattcacta cgggagtcgt cggcgagtca tccagtattt ttcctcgcga ctctctggcg
     3361 actcgccttc tctgaacacc agagcgacag tgtgttgagt catcgataaa tcaccgacga
     3421 ctcgttgccg agtcatccag tagtcgccga cgacccgctt ttgtataaat ctgaataaga
     3481 aaatacattt tttaaaacat aacaacctga tttaaaaaag aaatcagcaa aaagttagtt
     3541 ttgcgtgggg tgtgggcatc cggggcatga gaacagactt gcgtttttct ggaggaactg
     3601 cggggatttt tgattaaaca gtactcatcg cagagcggaa ttttatgcaa cgccggctgt
     3661 gctgcacggg gatttttaat cccccggccc gttattcatc tccacgggcg acggggatac
     3721 ataaacccga cagcagagga cgggtgagcg cgaatcccag agatgatgaa aaaagaggca
     3781 gagaaacgcg cccgggcacg ttttatctta ttgctgtggt gttgtccagg gtgtcggggc
     3841 tgtgccctga ccaggtggca tttgtctgat tgcgcgtgcg cggtccgaca aatgca
//
