LOCUS       NZ_CP120523             5743 bp    DNA     circular CON 08-APR-2024
DEFINITION  Enterobacter roggenkampii strain 0-E plasmid pER0-E3, complete
            sequence.
ACCESSION   NZ_CP120523
VERSION     NZ_CP120523.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN33770999
            Assembly: GCF_029536245.1
KEYWORDS    RefSeq.
SOURCE      Enterobacter roggenkampii
  ORGANISM  Enterobacter roggenkampii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Enterobacter; Enterobacter cloacae complex.
REFERENCE   1  (bases 1 to 5743)
  AUTHORS   Gauthier,J., Kukavica-Ibrulj,I., Cockenpot,L., Mohit,V., Brisson,C.
            and Levesque,R.C.
  TITLE     Complete Genome Sequence of Enterobacter roggenkampii 0-E
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 5743)
  AUTHORS   Gauthier,J., Kukavica-Ibrulj,I., Cockenpot,L., Mohit,V., Brisson,C.
            and Levesque,R.C.
  TITLE     Direct Submission
  JOURNAL   Submitted (23-MAR-2023) Institut de Biologie Integrative et des
            Systemes (IBIS), Universite Laval, 1030, avenue de la Medecine,
            Quebec City, QC G1V0A6, Canada
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: 04-JUL-2022
            Assembly Method                   :: Unicycler v. 0.4.8
            Assembly Name                     :: UL_Erog_v1.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 26.0x
            Sequencing Technology             :: Oxford Nanopore GridION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_029536245.1-RS_2024_04_08
            Annotation Date                   :: 04/08/2024 17:05:38
            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)                     :: 4,862
            CDSs (total)                      :: 4,747
            Genes (coding)                    :: 4,513
            CDSs (with protein)               :: 4,513
            Genes (RNA)                       :: 115
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 7
            Pseudo Genes (total)              :: 234
            CDSs (without protein)            :: 234
            Pseudo Genes (ambiguous residues) :: 0 of 234
            Pseudo Genes (frameshifted)       :: 156 of 234
            Pseudo Genes (incomplete)         :: 84 of 234
            Pseudo Genes (internal stop)      :: 25 of 234
            Pseudo Genes (multiple problems)  :: 27 of 234
            Pseudo Genes (short protein)      :: 1 of 234
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP120523.1.
            Bacteria and source DNA available from Institute of integrative and
            systems biology, Laval University, Quebec, Canada.
            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..5743
                     /organism="Enterobacter roggenkampii"
                     /mol_type="genomic DNA"
                     /strain="0-E"
                     /isolation_source="feces"
                     /host="Homo sapiens"
                     /db_xref="taxon:1812935"
                     /plasmid="pER0-E3"
                     /geo_loc_name="Canada: Quebec"
                     /lat_lon="46.8131 N 71.2075 W"
                     /collection_date="2022"
                     /collected_by="MELCCFFP"
     gene            complement(join(5382..5743,1..61))
                     /locus_tag="P3S52_RS01140"
                     /old_locus_tag="P3S52_01140"
     CDS             complement(join(5382..5743,1..61))
                     /locus_tag="P3S52_RS01140"
                     /old_locus_tag="P3S52_01140"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229777.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="helix-turn-helix domain-containing protein"
                     /protein_id="WP_061500298.1"
                     /translation="MARVSISEAARLVKVSRPTIYKMINSGKLSYTSVVKHGKGIKVID
                     TSELIRVFGSLDGVIDTVKYDVKSDAESTGINSVGLHDLQHRIALLEAENDGLKGAVKA
                     RDEHIDSLRQAMQLLEHKHEPSSPPHSPWWKFWKKS"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(61..252)
                     /locus_tag="P3S52_RS01145"
                     /old_locus_tag="P3S52_01145"
     CDS             complement(61..252)
                     /locus_tag="P3S52_RS01145"
                     /old_locus_tag="P3S52_01145"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000166328.1"
                     /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_032421723.1"
                     /translation="MTKQQKTALNMAKFIQNQSLLLLEKLNELDLDAEADLCEKLHDDA
                     EHLFRTLSSRLDELQDGN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(723..914)
                     /locus_tag="P3S52_RS01150"
                     /old_locus_tag="P3S52_01150"
     CDS             complement(723..914)
                     /locus_tag="P3S52_RS01150"
                     /old_locus_tag="P3S52_01150"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001041614.1"
                     /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_001041614.1"
                     /translation="MNKQQKTAVNMAKFIQDQSLLLLDRLNELDLDHEADFCEKLHEDA
                     ERLYRSLSARLNEQQDGA"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            complement(1808..2506)
                     /locus_tag="P3S52_RS01155"
                     /old_locus_tag="P3S52_01155"
                     /pseudo=""
     CDS             complement(1808..2506)
                     /locus_tag="P3S52_RS01155"
                     /old_locus_tag="P3S52_01155"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_076612230.1"
                     /GO_function="GO:0004803 - transposase activity [Evidence
                     IEA]"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="IS1 family transposase"
                     /name="IS1 family transposase"
     gene            2755..3387
                     /locus_tag="P3S52_RS01160"
                     /old_locus_tag="P3S52_01160"
     CDS             2755..3387
                     /locus_tag="P3S52_RS01160"
                     /old_locus_tag="P3S52_01160"
                     /inference="COORDINATES: protein motif:HMM:NF027277.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF4755 domain-containing protein"
                     /protein_id="WP_139137146.1"
                     /translation="MKIYYALKRIAYIAGALSIGCGSLPMIFSKTPALQYWVLGAFLIF
                     IGYCVSKLEFDKSKYIKYLNEKNDGIYIYYAKFGGEEHEIKINTKNKTIELKSGKNSAT
                     LNFDNIKSWRYNVSGISKVNVIGSTNSVMGNFTALSQASAINNQAGYSAWDNNGFFIHT
                     DALANPVWHIKIIPKDVAINLKSDKFWKSVAGECEVWMNVMNRAINK"
                     /name="DUF4755 domain-containing protein"
     gene            complement(<3398..3631)
                     /locus_tag="P3S52_RS01165"
                     /old_locus_tag="P3S52_01165"
                     /pseudo=""
     CDS             complement(<3398..3631)
                     /locus_tag="P3S52_RS01165"
                     /old_locus_tag="P3S52_01165"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_086558153.1"
                     /GO_process="GO:0006313 - DNA transposition [Evidence IEA]"
                     /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="IS1 family transposase"
                     /name="IS1 family transposase"
     gene            3788..4231
                     /locus_tag="P3S52_RS01170"
                     /old_locus_tag="P3S52_01170"
     CDS             3788..4231
                     /locus_tag="P3S52_RS01170"
                     /old_locus_tag="P3S52_01170"
                     /inference="COORDINATES: protein motif:HMM:NF024064.4"
                     /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="ribbon-helix-helix protein, CopG family"
                     /protein_id="WP_064188129.1"
                     /translation="MIAVSLPDELLQKLDNAVAKTGKKRSYLIRESIQMYLNQIENTHE
                     KKEIILNTSKPFYEILIEEFQVEKELMTEARKTEFTMFSDNGKLYVVNSKGNTRKLEAV
                     YVNNFFEEYKKTGSMSPSSYQDITFNSSYLLAALKYLIEKELI"
                     /name="ribbon-helix-helix protein, CopG family"
     gene            complement(4303..4575)
                     /locus_tag="P3S52_RS01175"
                     /old_locus_tag="P3S52_01175"
     CDS             complement(4303..4575)
                     /locus_tag="P3S52_RS01175"
                     /old_locus_tag="P3S52_01175"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004897311.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_019405140.1"
                     /translation="MATDAQVKEINALIKKYPDSCSICHEVYDEDDVTYTVFGYDRKGK
                     IQVTTGCCAGMLTEPVLLGVCGCFDPEERDEIMQNHPMAKQFFTE"
                     /name="hypothetical protein"
     Typing          790..1415
                     /name="rep_cluster_2327"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.627"
                     /coverage="99.0"
                     /evalue="1.1900000000000001e-169"
ORIGIN
        1 aaatagtagg gcgactaacc ttaacaagcc gtgctgcttc actaatagac actctggcca
       61 tcagttacca tcctgtaatt catccagtct cgaggacagt gtacggaaaa gatgctccgc
      121 atcatcgtgg agtttctcac aaaggtcggc ctcagcatcg agatcaagct cgttaagctt
      181 ctccagcagg agcagagact gattctggat gaatttagcc atgttcagcg ctgttttctg
      241 ttgtttcgtc ataagggacc tcagagcatc agtgctcagt gtaaaaccgg taagggggtc
      301 ggatgtacga atggttcaga gaacggatct gaggtaatcc tgtagttatt ttgtagttta
      361 tctgtagtca tcgcactaaa aatcaggatt aagtcatcag cttttgtagt ctttctgtag
      421 tttacctgta gtccggaaaa ataatccgtt catgcgagca tgaacgaggt cgttaatgac
      481 gtttttttgt caccgacgcc ccttaacctg cgtaaatcac ccgccatggt tgattatttt
      541 tcaacctcaa aatggtcata cacctaacgc agccgcgatt ttcatcgcaa cttcatgaaa
      601 aataaataaa aaagaaaaaa taaagggatt ctgggtatta ccggggtaat aatattaagc
      661 gccaggacaa tgaaaattaa ggcgatgccg gtattactcc ggtaataccc acaacggagc
      721 cattacgcac cgtcctgctg ctcattcagg cgcgctgaca ggcttcggta aaggcgttcc
      781 gcatcctcat ggagtttctc gcagaaatca gcctcatgat ccagatccag ctcattaagc
      841 ctgtccagaa gaagcaggga ctgatcctgg atgaatttag ccatgttaac ggcagtcttt
      901 tgttgtttgt tcatgaaggc cccggcgcga aagtgcttac tgtacgttct gatggttttc
      961 cgcttcctcg ctcattcgct cactccgttc ggtcatgagt ctgcggcgag cggaggaaga
     1021 tgagcagata acgtaacggt aagcataacg aaagctaagg acaagggcga aaaggccacg
     1081 ccccgccggg gcgcttttcc ataggctccg cccccctgac aagcatcacg aaatctgacg
     1141 ctcaaatcag tggtggcgaa acccgacagg actataaaga taccaggcgt ttccccctgg
     1201 tggctccctc gtgcgctctc ctgttcctgc ctttcggttt accggtgtca ttccgctgtt
     1261 atggccgcgt ttgtctcatt ccacgcctga cactcagttc cgggaaggca gttcgctcca
     1321 agctggactg tatgcacgaa ccccccgttc agtccgaccg ctgcgcctta tccggtaact
     1381 atcgtcttga gtccaatccg gaaagacacg acttatcgcc actggcagca gccactggta
     1441 acaggattca cggagcagag tagtagagtg cttctacaga gttcttgaag tggtggcctg
     1501 actgcggcta cactggaagg acagttttgg tatctgcgct ccgtgaaagc cagttacctt
     1561 cggaaaaaag agttggtagc tcttgattcc ggcaaacgaa ccaccgttgg tagcggtggt
     1621 ttttttgttt gcaggacatg agattacgac gcaacagaaa ggatctcaag aagttccttg
     1681 ctgtattgct actatcctag agatctgccc cattaggggc attatcagat gacggccttg
     1741 taatccacga taaaaaaccc agaaaccaga agagttggcc cagcgacata tgggtaatgc
     1801 tgccaactta ctgatagtgt tttatgttca gatagtgtcc gatgactttg tcatgcagct
     1861 ccaccgattt tgagaacgac agtgacttcc gtcccagcct tgccagatgt tgtctcagat
     1921 tcaggttatg tcgctcaatg cgctgagtat aacgcttgct gataacgtgg cagctttccc
     1981 ttcaggcgtg attcatacag cggccagcca tccgtcatcc ataccacgac ctcaaaggcc
     2041 gacagcaggc caagaagacg ctccagcgtg gccaacgtgc gttcaccgaa tacgtgcgcc
     2101 acaaccgtcc tccgtatcct gtcatacgcg taaaacagcc agcgctgacg tgatttagca
     2161 ccgacgtagc cccactgttc gtccatttca gcgcagacaa tcacatcact gcccggctgt
     2221 atgcgcgagg ttaccgactg cggcctgagt tttttaagtg acgtaaaatc gtgttgaggc
     2281 caacgcccat aatgcgggcg gttgcccggc atccaacacc attcatggcc atatcaatga
     2341 ttttctggtg cgtaccgggt tgagaagcgg tgtaagtgaa ctgcagttgc catgttttac
     2401 ggcagtgaga gcagagatag cgctgatgtc cggcagtgct tttgccgtta cgcaccaccc
     2461 cgtcagtagc tgaacaggag ggacaactga tagaaataga agccactgga gaacctcaaa
     2521 aacaccatca tacactaaat cagtaagttg gtatcatcac ctcaaagcca ttaggttcga
     2581 tttgaatata aacaattttc attaaactga tatttatcac caaattccga gccaaaagat
     2641 tacatcatat ttaaatgtaa tcttaaataa ctcagtgtat aattcaattg cacaataaga
     2701 attaacagtg tatttttagc caggaaatat gatttctaaa acggagattt aaaagtgaaa
     2761 atatattacg cattaaaaag aatagcgtat attgcaggtg ctttatctat tggttgcggc
     2821 tcactaccaa tgattttcag caaaacaccc gctcttcaat actgggtgct cggggctttt
     2881 ttaattttca ttgggtattg cgtatcaaag cttgagttcg ataagtctaa atacatcaag
     2941 tacctaaatg aaaagaacga tgggatttat atttattatg caaaatttgg tggcgaagag
     3001 cacgaaataa aaatcaacac aaaaaacaaa acaatcgaac taaagtcagg gaaaaattcc
     3061 gccacactaa actttgataa catcaaatca tggagatata acgtatctgg cattagcaag
     3121 gttaatgtca ttggttccac taacagcgta atgggtaatt tcacagcttt atctcaagcc
     3181 agtgcaatca acaaccaagc agggtacagc gcgtgggata ataatggatt ctttattcac
     3241 acagatgcat tggcaaatcc tgtctggcat ataaagataa taccaaaaga tgtcgcaata
     3301 aaccttaagt ctgacaagtt ttggaaaagt gtcgctggcg aatgcgaagt ctggatgaac
     3361 gtaatgaacc gagccattaa taaatagaag tcttactgtt gaggccagcg cccgtgatac
     3421 gggcactggc acagcaccca ataccattca cgggcatatc aatgattttc tggtgcgcac
     3481 cgggctgaga ggcggtgtaa gtgaactgta gttgccatgt tttacggcaa tgagagcaga
     3541 gatagcgctg atgtccggca gtgcttttgc cgttacgcac cacgccttca gtagcggagc
     3601 aggaaggaca tctgatggaa atggaagcca cgcaagcacc ttaaaatcac catcatacac
     3661 taaatcagta agttggcagt attacccaca catagttgat taaaaaagag gcctcaccca
     3721 ttgacgaaca tctaatttta tataaaatta gatgaatcga atagacgtta actatagagg
     3781 catccaaatg atagcagtat cacttcctga cgaattactg caaaaactag ataacgctgt
     3841 agctaaaaca ggcaaaaaac gctcttattt aatcagggaa tcaatacaga tgtatttgaa
     3901 tcaaatagaa aatacacatg aaaaaaaaga gattatcctg aacacctcaa aaccgttcta
     3961 tgagatccta attgaggaat ttcaagttga aaaagaactg atgactgagg ccagaaagac
     4021 tgagttcacg atgtttagtg ataacggaaa actctatgtg gtaaattcga aaggaaatac
     4081 acgcaagtta gaagccgtct acgtaaataa tttctttgaa gagtataaga aaacaggaag
     4141 catgagccca tccagctatc aagatataac cttcaactca tcttatcttt tagcagcgct
     4201 aaagtacctg atagaaaaag aactgattta acataaaccc tcatttcacg cagatatgaa
     4261 aaagcccgca caaggcgggc ttcagactca acagatacgg aatcactctg tgaaaaactg
     4321 ctttgccatg gggtgattct gcatgatctc gtcacgttct tccgggtcaa agcacccaca
     4381 gacacccagc agaaccggct ctgtcagcat tccggcacag catcccgtgg tgacctgtat
     4441 tttacctttc cggtcatacc caaaaacggt gtaggtcaca tcatcctcat catagacttc
     4501 atgacagatg gagcatgagt ctgggtattt tttgatgagt gcattaattt cttttacctg
     4561 agcgtcagta gccaaaacat ctccctgagt cactgattat cacaatccgc tgactctaac
     4621 acagactcag gcatccgccg ttgatttacc ataacgtccc attacgcgca ccgcgaaaac
     4681 ggcctcaggg cgtttctgac gggaaaccgg taaaacaggc aacaaccccc cccgaaaacc
     4741 cgccagaaac gcgcaggctc tgtttttacg gcatgcatga gtatgcgcgc aagtgcatag
     4801 cgcggaaatt cacgccattc agccggggta agtcctgttt ccgatgttct tcttacccga
     4861 aaacggtgaa cggggacgca atttattgcg tggccgtgaa gcgttgccgg cgcagccgga
     4921 aaaccggttt tcagcacgtt caggaatcgg gttcgtcgac ggccggcaat cacgttatgg
     4981 caagtcgccg gacgactcac cacacgattc accggcgatt cgactcgtga cttgactcta
     5041 gagtcaccac ggtcataaaa acgccaaagc gacgattcga ctctagagtc aagtcgtcat
     5101 aagttactga tagtgtggag tgagtcgtcg atgactctat gacgagtcgt cggcaagtcg
     5161 tacacgaatc accgacgact tggattgacc ttacagaagg taatactgcg taatttaata
     5221 aaacctaacc aactgataat aaggagttat ctgcaaaatt ttaattttgc gtggtgtgtg
     5281 ggtatttttc gtggtgagga gtgttcccgg atctggcgat ttttgggaag gttcaggaac
     5341 gccccgggat ggccggagag gaaaactcaa gcatggcggg atcaggattt tttccagaat
     5401 ttccaccacg gggaatgggg tggtgaagaa ggttcgtgct tgtgctccag aagctgcata
     5461 gcctgacgaa gggaatcaat atgctcatct cgagccttaa cagccccttt aagaccatcg
     5521 ttttcagctt caagtaaagc gattctatgt tgtaaatcat gtaaaccaac gctgttaata
     5581 cctgtagatt ctgcgtcact ttttacatca tattttacag tatcgatgac accatcaaga
     5641 gaaccaaaca ctctaataag ctctgatgta tcaataactt taataccctt cccgtgcttt
     5701 acaacagagg tgtaacttaa cttaccactg ttaatcatct tgt
//
