LOCUS       NZ_CP066842             5463 bp    DNA     circular CON 27-MAY-2024
DEFINITION  Escherichia coli strain Ec-RL2-1X plasmid pCol156, complete
            sequence.
ACCESSION   NZ_CP066842
VERSION     NZ_CP066842.1
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 5463)
  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  JOURNAL   Unpublished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 5463)
  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
            CP066842.1.
            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..5463
                     /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="pCol156"
                     /geo_loc_name="USA: Athens, GA"
                     /lat_lon="33.90687937 N 83.37872475 W"
                     /collection_date="2018-04-16"
     gene            complement(18..1037)
                     /locus_tag="JH656_RS24480"
                     /old_locus_tag="JH656_24255"
     CDS             complement(18..1037)
                     /locus_tag="JH656_RS24480"
                     /old_locus_tag="JH656_24255"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221104.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /protein_id="WP_001271364.1"
                     /translation="MSAALQYFEENLPHRPYHTDDLAFGLRISGKGRALLARYIQQNQP
                     HAQFWLVFDVDREGAAIDWSDRNAPAPNITVKNPVNGHAHLLYALNIAVRTAPDASVKA
                     LKYAAAVERSLCEKLCADVNYSGLICKNPFHLEWQVMEWREDAYTLDELADYLDLSASE
                     RRSIDKHYGMGRNCHLFEMTRKWAYRAIRQGWPAFSQWLEAVIQRVEMYNASLPVPLSL
                     AECRAIGKSIAKYTHRNFTPETFAQYVADTHTPEIQAARGRKGGKANSSENQSDKGKKS
                     AAVRWTANDDKRRRALDMYILGASTEDIAVAVGVSSRTIRRWMDNSGEWLTKKQIIKC"
                     /name="replication initiation protein"
     gene            complement(1838..2962)
                     /locus_tag="JH656_RS24485"
                     /old_locus_tag="JH656_24260"
     CDS             complement(1838..2962)
                     /locus_tag="JH656_RS24485"
                     /old_locus_tag="JH656_24260"
                     /inference="COORDINATES: protein motif:HMM:NF013211.4"
                     /GO_component="GO:0016020 - membrane [Evidence IEA]"
                     /GO_function="GO:0140911 - pore-forming activity [Evidence
                     IEA]"
                     /GO_process="GO:0019835 - cytolysis [Evidence IEA];
                     GO:0050829 - defense response to Gram-negative bacterium
                     [Evidence IEA]; GO:0031640 - killing of cells of another
                     organism [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="colicin-like pore-forming protein"
                     /protein_id="WP_021529456.1"
                     /translation="MSGGDGRGPGNTGLGHNGGKPSGNVNGSSGHGGPSSGGGYHYNPG
                     KGPASTVGPDGEVHINITGGMEKDPPGKHHGNGGSGNGHGAGNHNSNSGGNGKTTSIPG
                     WSPDSGKPGRYLPTNKDKLIKGLIQSIDDHSGTYTIHYTGGAVATVTVPNGDVNKMNVH
                     YNIGSGPSSGNKLTRDTIKSFLEFKAENEANAVNDAISKVNDFYKELASKYGDKLEKEA
                     KALADEAKGKKIRNANEAIKAFDRYKDVLNKKFSVSDREAIAKALESLNKDQMAKQLKI
                     FGKAFGVVGEAIQWGGFISGLVKGFRTGDWNEAFISGEKIAVGKVASVMVTVAFSAMAV
                     NPIGILGFAVIMAVTSALITDERLKQLNSFINGI"
                     /name="colicin-like pore-forming protein"
     gene            complement(3183..3716)
                     /locus_tag="JH656_RS24490"
                     /old_locus_tag="JH656_24265"
     CDS             complement(3183..3716)
                     /locus_tag="JH656_RS24490"
                     /old_locus_tag="JH656_24265"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221103.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_000168774.1"
                     /translation="MASTEEKLLTLLLSVEHLQHTAMEQQKAVADSLAVARETLRGYRD
                     ISDGVAKQVRDEVRNEVQNLDVAGLIGERISQDFQRLEESVANMKANADALNRDIATIH
                     SNIVQEYNTLKGYSWKWLGGVSVAFLVMFCVLGWGMKTMLDRNYNATAAVYQKVVILED
                     KLAEKPVTGKNRKN"
                     /name="hypothetical protein"
     gene            complement(3719..4645)
                     /locus_tag="JH656_RS24495"
                     /old_locus_tag="JH656_24270"
     CDS             complement(3719..4645)
                     /locus_tag="JH656_RS24495"
                     /old_locus_tag="JH656_24270"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005221102.1"
                     /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="WP_001736644.1"
                     /translation="MATYHLSVKFGGKGQAANHADYIERKEKYRDRQDLEYSAHGNMPE
                     WARDNPSHFWQAADQFERANGSTYRELEIALPRELTPEQRLELVQDFVRQEAGERHAWS
                     FAIHNPKASIEGGEQPHAHIMMSQRVNDGIERTPEQYFRRYNARYPERGGAKKDSGSLT
                     PTQQKEQLRELRKRWEVKHNEHMRKNGFERGFIDCRTLKEQGIERRPEVHLGFEAAGRL
                     DDAQRHDIMQKRSEPDYSRHLEQARTVGHDIMEWLDTPVKQHELVRRLQHDVAREHGFD
                     MRDRVSRQDRTEPERVKSPSRGFSMGF"
                     /name="MobA/MobL family protein"
     gene            4822..5220
                     /locus_tag="JH656_RS24500"
                     /old_locus_tag="JH656_24275"
     CDS             4822..5220
                     /locus_tag="JH656_RS24500"
                     /old_locus_tag="JH656_24275"
                     /inference="COORDINATES: ab initio prediction:GeneMarkS-2+"
                     /note="Derived by automated computational analysis using
                     gene prediction method: GeneMarkS-2+."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_001222916.1"
                     /translation="MRISNIEWLKKRIGFIRKLGEQTARQRQIIDLLDNEAGLTEQERK
                     LLHVLATAEKNDLQAQESERKQAVQKRIEGKKQRRERNHRLFLAAGLLIEAGLVDTKTG
                     ELCYKKDRILQALKEIKYDLETSPNPDA"
                     /name="hypothetical protein"
     Typing          complement(263..1037)
                     /name="Col156"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="96.907"
                     /coverage="83.0"
                     /evalue="0.0"
     Typing          complement(3723..4645)
                     /name="MOBQ"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.052"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgttgcttct ttgttaacta acatttaatt atttgtttct tggttagcca ttctccagaa
       61 ttatccatcc agcgtcgaat agtccggctg ctaacaccaa ccgccactgc aatatcttcc
      121 gttgacgctc ccaagatata catatcaagc gccctacgac gtttgtcgtc gttagcagtc
      181 caccgaacag cggcgctttt tttccctttg tccgactgat tttctgacga attggccttc
      241 ccgcccttgc gaccgcgtgc tgcctgaatt tctggcgtgt gcgtatcagc cacatactgt
      301 gcgaaagttt ccggcgtgaa gttcctgtgc gtgtatttcg caatgctctt gccaatagcc
      361 cgacattcag ccagtgaaag cggaacggga agcgatgcat tgtacatttc gacacgctgg
      421 atcaccgctt caagccactg tgagaacgct ggccagccct gacgaatcgc cctgtaagcc
      481 catttgcgcg tcatttcgaa caggtggcag tttcgcccca tcccgtaatg tttatcgatg
      541 ctacgacgct ctgaggcgct caaatcgaga taatctgcca gttcatcgag ggtataggcg
      601 tcctcgcgcc actccatcac ctgccattcc aggtggaacg gatttttgca aatcaggccg
      661 ctgtagttca catcagcaca aagtttctca cacagcgaac gttcaaccgc tgcggcatat
      721 ttcagcgcct taaccgaggc atcaggcgcg gttctcacgg cgatgttgag tgcgtagagc
      781 aggtgagcgt gtccgttcac aggattttta acggtgatgt tcggcgcggg ggcgttccgg
      841 tcgctccagt caatcgcagc cccctcgcgg tcaacgtcaa aaaccagcca gaactgcgca
      901 tgaggctggt tctgctggat gtaccgcgca agaagcgcac gccctttgcc ggagatgcga
      961 aggccgaaag cgagatcatc cgtgtgatag gggcggtggg gtaaattttc ttcgaagtat
     1021 tgaagcgcgg cgctcatgtg ttacgattcc ttccaggtta tcgaccgacc tcgcccctgt
     1081 attctcgtga caatcttggc ggagagacac gaatttcagg ggcgtttgtt tttcagtcgc
     1141 ttacactacc cccaacaaca aaacctgtcg agccttcccg caaaaccgat ccatttacca
     1201 taactcccgt tgtacgtacc ccttaaaacg ccctcagtcg ctttctggcg caaaaaatgc
     1261 aaaaagacaa ggaaacacca ggccaaacca gaaaaatgcg tcagaatcac tttcagggcg
     1321 ttgcataact atgcacgaaa gcgattcgca aacagtttcg accgttcaaa agggcgaacg
     1381 agtcaaaaaa gtaacttttg tgataactac ttctagattt atggataaag taaggcaata
     1441 ttataaacat ttaactaacg aggattttat aaatgaaaaa aatagatatg gaattctatt
     1501 taaggaattt tatccttgcc ttatcctttt acattttatc ttttatcatc gcaagtttga
     1561 atctaagccc aacaagtata gaattattta tatttatact tatatctctt tttggatcgt
     1621 ccacataccc tttttgtcta ttactaataa ataagcaagc acccttacta acaaaaacaa
     1681 cttttaactt cgttaactgg ggttttataa tatgcattat attatcacta cctccatttg
     1741 gattgatttt tacagtctat tactttataa ccaacaaaaa gcgatagaaa aacaaaataa
     1801 aggtcatacc atatcaaacg gtacgacctt ttgtttatta aatgccgtta ataaagctgt
     1861 ttagttgttt cagcctttca tctgtaatta aggcactagt cactgccata attactgcaa
     1921 accctaaaat accaatagga tttactgcca tagcactaaa tgccactgta accataacag
     1981 atgctacctt gccgactgcg attttttccc cgcttataaa agcctcattc cagtcaccag
     2041 ttctgaatcc tttaactaag ccactgataa atccccccca ctgaatagcc tcacctacga
     2101 caccaaaggc cttaccaaaa atttttaact gtttagccat ttgatcttta ttaagagact
     2161 ccagtgcttt tgcaatcgct tctcggtcgg atacgctgaa tttcttatta agcacatcct
     2221 tgtacctatc aaaggcttta atcgcctcat tagcattgcg aatttttttc cctttagctt
     2281 catcggctag tgccttggct tctttctcca acttatcgcc gtattttgat gctaactctt
     2341 tataaaagtc attaactttg cttattgcat catttacagc attagcttca ttttctgcct
     2401 tgaattctaa aaagcttttt atagtatcac gagtcagttt attacctgat gacggcccac
     2461 taccgatatt atagtgaaca ttcattttat tcacatcacc gtttggtaca gttactgtag
     2521 ctactgcacc accagtataa tggatagtgt acgttccaga atggtcatct attgactgaa
     2581 taagtccctt aattaactta tctttatttg tcggtaaata tctgccaggt ttcccagagt
     2641 cagggctcca tccaggaata gacgttgttt ttccattgcc gcctgaattg ctgttatgat
     2701 ttccagcacc gtgaccatta cctgagccac cattaccgtg atgttttcct ggaggatctt
     2761 tttccatacc accggtaatg ttgatatgca cctccccgtc aggacctaca gtgcttgcag
     2821 gaccttttcc cggattgtaa tgatacccac cgccagatga tggtcctcca tgtccagatg
     2881 agccattcac gtttccactg ggtttaccac cgttatgtcc aagccctgta ttaccagggc
     2941 cacgaccatc tccaccactc ataaaaattc cctcttttaa tcgttaaaac aattaattac
     3001 atagttaata ctgtacataa aaccactggt tttatgtaca gatcaaaaag tactcgccat
     3061 tattttttct gtcaagtcag ggagggatat tttttggcag ttcggaggaa tcactcatga
     3121 aaacggtgaa cggaacgcga aatcctttcg ctgtccgtga ggcgttggac aagcgaagcg
     3181 cgtcagtttt tccggttctt acccgtgaca ggtttttccg ccagtttatc ttccagtatc
     3241 acaactttct gatacaccgc cgctgtggcg ttgtagttcc tgtcgagcat tgttttcatt
     3301 ccccatccga gcacacagaa cataactaga aaagccactg acaccccacc cagccatttc
     3361 cagctatacc ctttaagggt gttgtattcc tgcacgatat tgctgtgaat tgtcgcaata
     3421 tccctgttca gggcatccgc gtttgccttc atgtttgcga ctgactcttc cagccgctga
     3481 aaatcctggc tgatgcgctc acctatcagc cctgctacgt ccagattctg cacctcattt
     3541 ctgacttcat ccctgacctg ttttgccaca ccgtcagaaa tatcccgata tccgcgaagt
     3601 gtttcccttg ccacagccag agaatcagca acagctttct gttgctccat tgcggtatgt
     3661 tgcaaatgct ccaccgataa caggagcgtg agtaattttt cttctgtgct ggccatgttc
     3721 agaatcccat agaaaatcca cgtgacggtg atttaacccg ttcaggttca gttcggtcct
     3781 gtctgctcac tctgtctctc atgtcaaagc catgctcccg cgcaacatca tgttgcagcc
     3841 ttctgaccag ttcatgttgc ttaaccggag tgtccagcca ttccatgatg tcatgcccga
     3901 ccgttcgcgc ctgttcaaga tggcgggaat agtccggttc agaccgtttt tgcatgatgt
     3961 catgacgctg ggcatcatca agccgtccgg cagcttcaaa acccagatgc acttcgggac
     4021 gtcgttcaat gccctgttct ttcagcgtcc gacagtcaat gaagcccctt tcaaagccat
     4081 tttttctcat atgttcgttg tgcttcacct cccagcgttt tcgcaattcc cgcaactgct
     4141 ctttttgctg agtgggagtc aggcttcctg aatccttttt cgcacctccc cgctcgggat
     4201 acctggcgtt atagcgccgg aaatactgtt ccggtgtacg ttcaatgcca tcattcacac
     4261 gctgactcat catgatatgc gcatgaggct gttcgcctcc ctcaatgctc gctttcggat
     4321 tgtgaatggc aaaactccat gcatgccgtt cgccagcttc ctgacgtaca aaatcctgca
     4381 ccagttcaag gcgctgttcc ggtgtcagtt cacggggcag cgctatctcc agttcccgat
     4441 aagtcgaacc gtttgcacgt tcaaactggt cagccgcctg ccagaaatgg gagggattat
     4501 ctcgcgccca ttccggcatg tttccgtgtg cggaatattc caaatcttga cggtcgcggt
     4561 atttctcttt gcgctcgatg taatcggcat ggtttgcagc ctgtcccttg ccaccaaact
     4621 taacgctgag gtgataggtc gccacggttt cagccctccg caggagcgca ctgtttctcg
     4681 acgaaggaga gaaacatata agtgcgcttc cttctaattt tacgaattag cacggaagat
     4741 accccctgca cccgccgacc gcaagcgata tactgcacga ccacaacaca ccgcaaaaaa
     4801 acaccaggga gcaccacgaa catgcgcatc agcaacatcg aatggctgaa gaaacggatc
     4861 ggattcatca ggaagctcgg agaacagacc gcacgacaga gacagattat tgacctgctc
     4921 gacaacgaag caggactcac agaacaggaa cgcaaactcc tccacgtact ggcaacagcg
     4981 gaaaaaaacg acttacaggc acaggagagc gaacgaaaac aggcggtcca aaaacgaatc
     5041 gagggaaaaa aacaacgacg agaacgcaat caccgactct ttctcgcggc tgggctactg
     5101 atcgaagcag gactggtaga cacaaaaaca ggcgagctat gctataaaaa agacaggata
     5161 ttacaggcac ttaaggaaat taagtacgat ctggagacat ccccaaaccc agacgcgtaa
     5221 gtgcctccat ccgtgttccg gttccctggt gcttcctcgc tcattcgctc gctacgctcg
     5281 gtcatgagac tgcggcgagc acgaccacct caatcatgcg gtaagccgca ccattgctgg
     5341 gctgagagga gaaaaccgcc ggaaagcccg ctgctcaaaa agacgccgaa aggcgctgtt
     5401 atctgatata ggcttgttca tgtccgcgaa tttaacatcc cattaacaaa aaacaggggg
     5461 tag
//
