LOCUS       NZ_CP066843             4051 bp    DNA     circular CON 27-MAY-2024
DEFINITION  Escherichia coli strain Ec-RL2-1X plasmid pCol, complete sequence.
ACCESSION   NZ_CP066843
VERSION     NZ_CP066843.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN17168892
            Assembly: GCF_022695865.1
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1  (bases 1 to 4051)
  AUTHORS   Oladeinde,A.
  TITLE     Conjugation and transduction are the main drivers of antimicrobial
            resistance in Salmonella enterica serovar Heidelberg
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4051)
  AUTHORS   Oladeinde,A.
  TITLE     Direct Submission
  JOURNAL   Submitted (30-DEC-2020) ARS, USDA, 950 College Station Rd, Athens,
            GA 30605, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 19-MAR-2020
            Assembly Method                   :: Unicycler v. v0.4.8
            Assembly Name                     :: Ec-RL-1X
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 1.0x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_022695865.1-RS_2024_05_27
            Annotation Date                   :: 05/27/2024 04:46:12
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,923
            CDSs (total)                      :: 4,806
            Genes (coding)                    :: 4,539
            CDSs (with protein)               :: 4,539
            Genes (RNA)                       :: 117
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 86
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 267
            CDSs (without protein)            :: 267
            Pseudo Genes (ambiguous residues) :: 0 of 267
            Pseudo Genes (frameshifted)       :: 61 of 267
            Pseudo Genes (incomplete)         :: 209 of 267
            Pseudo Genes (internal stop)      :: 43 of 267
            Pseudo Genes (multiple problems)  :: 43 of 267
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP066843.1.
            Bacteria and source DNA available from Adelumola Oladeinde.
            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..4051
                     /organism="Escherichia coli"
                     /mol_type="genomic DNA"
                     /strain="Ec-RL2-1X"
                     /isolation_source="cecum of Ec-RL2-1X 2-week old broiler
                     chicken on used pine shavings infected with Salmonella
                     enterica serovar Heidelberg"
                     /host="Gallus gallus domesticus"
                     /db_xref="taxon:562"
                     /plasmid="pCol"
                     /geo_loc_name="USA: Athens, GA"
                     /lat_lon="33.90687937 N 83.37872475 W"
                     /collection_date="2018-04-16"
     gene            442..1581
                     /locus_tag="JH656_RS24505"
                     /old_locus_tag="JH656_24280"
     CDS             442..1581
                     /locus_tag="JH656_RS24505"
                     /old_locus_tag="JH656_24280"
                     /EC_number="2.7.7.49"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000900598.1"
                     /GO_function="GO:0003964 - RNA-directed DNA polymerase
                     activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="reverse transcriptase family protein"
                     /protein_id="WP_005761319.1"
                     /translation="MNKPRFNGTPVASLDSLSAMLGIERKRLDWIVKSVSMSYKQFKVE
                     TGKNKKERQIFEPKRSLKGIQKKINKEIFEKIDYPHYLHGALSGRDYISNAAVHTRKRT
                     VICLDITNFYPSISKKDVCSIFKNLMRFSPDVSLCLTELVTLNNKVPQGGCCSSYIANL
                     LFFNSEYNLYNRLKSMGLSYSRLLDDITISSDKDLSSEEKTKVIKLVHGMVNQYRLSIN
                     ESKTTIEHSKDSSSKLSVTGLWVKHGVPKLTKENRRYIRYLVYICKKQGAYERHTKEYH
                     DLWNRCSGKVAQMSRLGHVQAVELRAILSEIMPVYDDYKISKLKLMAKHYLNKFTPPLT
                     DDQIRKIDRMLYDFDIVGRTNKNLAKLYRRKLVALLPDR"
                     /name="reverse transcriptase family protein"
     gene            1586..1789
                     /locus_tag="JH656_RS24510"
                     /old_locus_tag="JH656_24285"
     CDS             1586..1789
                     /locus_tag="JH656_RS24510"
                     /old_locus_tag="JH656_24285"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000427298.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="retron Se72 family effector protein"
                     /protein_id="WP_000427298.1"
                     /translation="MENGFVNFYDHVKGYGFIRRERGRDVFFRYDDFLFLGHDVDICKG
                     ILVRFKLEKTDKGFKAVAIQKV"
                     /name="retron Se72 family effector protein"
     gene            complement(2627..2821)
                     /locus_tag="JH656_RS24515"
                     /old_locus_tag="JH656_24290"
     CDS             complement(2627..2821)
                     /locus_tag="JH656_RS24515"
                     /old_locus_tag="JH656_24290"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041624.1"
                     /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_001041640.1"
                     /translation="MNKQQQTVLNMAGFIKSQSLTLLEKLDALDADEQAAMCEKLHELA
                     EELQNSIQTRFEAENRTGI"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            3105..3428
                     /gene="mobA"
                     /locus_tag="JH656_RS24520"
                     /old_locus_tag="JH656_24295"
     CDS             3105..3428
                     /gene="mobA"
                     /locus_tag="JH656_RS24520"
                     /old_locus_tag="JH656_24295"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:NP_052604.1"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="plasmid mobilization protein MobA"
                     /protein_id="WP_000166966.1"
                     /translation="MTKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRA
                     AALGKKVNSLTDDRVLKEVMRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRL
                     MAD"
                     /name="mobA"
     gene            3653..3919
                     /locus_tag="JH656_RS24525"
                     /old_locus_tag="JH656_24300"
     CDS             3653..3919
                     /locus_tag="JH656_RS24525"
                     /old_locus_tag="JH656_24300"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001243419.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_224471576.1"
                     /translation="MVKLLLVRNEYFNKNNDLKTVARFDGKTLRDAFSRKIATFDGKVL
                     RDASLKKVATFDGQNLRDASSKIILSADAEVGIVVMAFVAELI"
                     /name="hypothetical protein"
     Typing          2857..3096
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="99.17"
                     /coverage="100.0"
                     /evalue="1.65e-119"
     Typing          complement(2071..2592)
                     /name="rep_cluster_2350"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.476"
                     /coverage="95.0"
                     /evalue="0.0"
     Typing          3106..3425
                     /name="MOBF"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="99.065"
                     /coverage="100.0"
                     /evalue="3.08e-62"
ORIGIN
        1 tggttacgtg tatgttgcgc aaggaaaccg atgccttgtt tttaaggcga tctcgcatga
       61 gatcatgacc ggcctggccg ctaattaatg gtgagaacgc ccctgagcgt gtatcagcac
      121 taaaagaata gcgacgattg tctggcaatg tgagttaaaa gtcccaaaga gccaatagag
      181 tttttccttg ctttcctact ggtctggcaa aatttcataa ccaataggag ttgcatcatg
      241 tttattatca acatcaacat taacgtaacc aagagctctt catcttgttc tggagacggt
      301 cagatgaaga aaaaaagaga ggttggctct ctggaggcac tgaaaaaaac acagtttttg
      361 ttttctatgt gcttgattat gtttaaagta atagattacg tatcgaaact ttttaactaa
      421 tcgactttta actcaaacat catgaataaa cccaggttta atggaactcc tgttgcatct
      481 ttggattctt tatctgcgat gttaggcata gaaagaaaaa gattggactg gatagtcaag
      541 tctgtatcga tgtcgtacaa gcagtttaag gttgaaacag ggaagaataa aaaagaaagg
      601 caaatttttg aacccaagag atctttgaaa ggaattcaaa aaaaaataaa taaagagatt
      661 tttgagaaaa ttgattaccc tcattatttg catggggcgt taagtggtcg cgattatata
      721 tctaatgccg ctgttcatac taggaaaaga acagttatat gtcttgatat caccaatttt
      781 tatcccagca ttagtaaaaa agatgtttgt tctattttta aaaatttaat gcgtttttct
      841 cctgatgttt ctttatgctt aacggaactt gtgacgttga ataataaggt ccctcagggt
      901 gggtgctgtt ctagttatat tgcaaatctt ttatttttta atagtgagta taatctctat
      961 aatagattga agtctatggg gctttcatat tcaaggcttt tagatgatat tactatatcc
     1021 tctgataagg atctttcatc agaggaaaaa acaaaagtaa taaaactcgt tcacggaatg
     1081 gtgaatcagt acagactttc aataaatgaa agtaagacaa cgatagagca ctcaaaagat
     1141 tcgtcttcta aacttagtgt cactgggttg tgggtaaagc atggtgttcc taagttaaca
     1201 aaagaaaata gacgttatat caggtactta gtttatatat gtaaaaaaca aggtgcttat
     1261 gaacgtcata cgaaagagta ccatgattta tggaatagat gctctggcaa ggttgctcaa
     1321 atgtcgaggc ttgggcatgt ccaggcggtt gaattgaggg cgattctttc tgagataatg
     1381 ccagtttatg atgattacaa gatatctaaa ttaaagttga tggctaagca ctatctaaat
     1441 aagtttacgc cgcctttaac tgatgatcag attaggaaaa tagataggat gctctatgat
     1501 tttgatatag tagggcggac taataagaat cttgcaaaac tatatagacg taagctcgtg
     1561 gcattacttc cagataggtg attatatgga aaatggattt gttaattttt atgaccatgt
     1621 taaagggtat ggctttataa ggcgtgagcg tggacgtgat gttttctttc ggtatgatga
     1681 ttttttgttt ttagggcatg atgtcgatat atgtaaaggt attttagtta ggtttaaatt
     1741 agaaaaaaca gataaagggt ttaaagctgt agcgattcaa aaggtataac atcgtggatg
     1801 tgtcagcttg tttttatgat atgagaactt gagatccttt ctatctcgtc gtaatctctt
     1861 gctgtgtaaa cgaaaaaacc gccttgcagg gcggtttttc gaaggttctc agagctacca
     1921 actctttgag ccgaggtaac tggcttggag gagcgcagtc accaaaactt gttctttcag
     1981 tttagcctta acaggcgcat gacttcaagg ctaactcctc taattcggtt accagtggct
     2041 gctgccagtg gcgataagtc gtgtcttctc ggtttggatt caagtcgata gttaccggat
     2101 aaggcgcagc ggtcggactg aacggggggt tcgtgcatac agtccagctt ggagcgaacg
     2161 acctacaccg ggccgagata ccaacagcgt gagctatgag aaagcgccac gtttcccgaa
     2221 gggagaaagg cggacaggta tccggtaagc ggcagggtcg gaacaggaga gcgcacgagg
     2281 gagcttccag ggggaaacgc ctggtatctt tatagtcctg tcgggtttcg ccacctctga
     2341 cttgagcgtc ggtttttgtg atgctcgtca ggggggcgga gcctatggaa aaacgccatc
     2401 ggcgcggcct ttgtccctgg cttcggcttt ttgctcacat gttctttccg gcgttatccc
     2461 ctgattctgt ggataaccgt attaccgcct ttgagtgagc tgacaccgct cgccgcagtc
     2521 gaacgaccga gcgtagcgag tcagtgagcg aggaagcgga agagcgcctt atgtgacatt
     2581 ttctccttac gctcctctat gccgttctgc atcctgtccg gatgcgttat atcccggtgc
     2641 gattttccgc ttcaaagcgt gtctgtatgc tgttctgaag ttcttccgcg agttcgtgca
     2701 gcttctcaca catggcggcc tgttcgtcag catcaagtgc gtccagtttt tcgagcagcg
     2761 tcaggctctg gctttttatg aatcctgcca tgttgagtac ggtttgctgc tgcttgttca
     2821 tctttctgtt ttctccgttc tttctgtcat ctgcgttgtg tgattatatc gcgtaccact
     2881 tttcgactgt tttaccgtcg gtattctgct gtctgactct ttgacgggca tttctgtcag
     2941 acaacactgt cactgccaaa aaactgccgt gcctttgtcg gtaattcgag cttgctgaca
     3001 ggacaggatg tgcaattgtt ataccgcgca tacatgcacg ctattacaat taccctggtc
     3061 agggctttgc cccgacaccc atgtcagata cggagccatg ttttatgaca aaacgaagtg
     3121 gaagtaatac gcgcaggcgg gctatcagtc gccctgttcg tctgacggca gaagaagacc
     3181 aggaaatcag aaaaagggct gctgaatgcg gcaagaccgt ttccggtttt ttacgggcgg
     3241 cagctctcgg taagaaagtt aactcactga ctgatgatcg ggtactgaaa gaagttatga
     3301 gactgggggc gttacagaaa aaactcttta tcgacggcaa gcgtgtcggg gacagggagt
     3361 atgcggaggt gctgatcgct attacggagt atcaccgtgc cctgttatcc aggcttatgg
     3421 cagattagct tccaggggag aaaactgtcg aaaacagacg gtatgaacac tgtaagctcc
     3481 caaagtgatc accactcgct ttcatgcata gctatgcagc gagctgaaaa cgatcctgac
     3541 gcatttcccc ggttttctta gggtaaaaca tctctttttg cagtgtctgt gtcagaatcg
     3601 cgctgagcgc gattctgtgg tgcgtacaat taagggatta tggtaaatac aattggttaa
     3661 attactattg gtgagaaatg aatatttcaa taaaaacaat gacttaaaaa ccgttgctcg
     3721 gtttgacggt aaaaccttaa gagatgcctt ttcgagaaaa atagcgactt ttgatggcaa
     3781 ggttttaagg gatgcctctt taaaaaaagt agcaaccttt gacggtcaga atttaagaga
     3841 tgctagttca aaaattatcc tgagtgccga tgctgaggtt gggattgttg ttatggcctt
     3901 tgtagctgag ttgatttgaa tctcatgctg catacctttt agcctatcgc tggcaggata
     3961 aggcgctttc ttgttggtga cagaaagata aaaaacttta taataatcag cgaagcgggc
     4021 gaaccacgcc tggctctcgc tctttaacaa a
//
