LOCUS       NZ_CP110781             3576 bp    DNA     circular CON 09-JUL-2023
DEFINITION  Citrobacter freundii strain Cf-Emp plasmid pCf-unmd7, complete
            sequence.
ACCESSION   NZ_CP110781
VERSION     NZ_CP110781.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN31656063
            Assembly: GCF_030064365.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 3576)
  AUTHORS   Riccobono,E., Salvetti,S., Coppi,M., Montenora,I., Di Pilato,V. and
            Rossolini,G.M.
  TITLE     Citrobacter freundii resistant to novel beta-lactamase inhibitor
            combinations and cefiderocol, co-producing class A, B and D
            carbapenemases encoded by transferable plasmids
  JOURNAL   J Antimicrob Chemother 78 (7), 1677-1682 (2023)
   PUBMED   37207353
REFERENCE   2  (bases 1 to 3576)
  AUTHORS   Di Pilato,V., Coppi,M., Riccobono,E., Salvetti,S., Montenora,I. and
            Rossolini,G.M.
  TITLE     Direct Submission
  JOURNAL   Submitted (08-NOV-2022) Department of Surgical Sciences and
            Integrated Diagnostics (DISC), University of Genoa, V. Benedetto XV,
            6, Genoa, Italy 16132, Italy
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Date                     :: DEC-2021
            Assembly Method                   :: Unicycler v. 0.4.8
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 115.0x
            Sequencing Technology :: Illumina NovaSeq; Oxford Nanopore MinION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 07/09/2023 10:07:47
            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)                     :: 5,602
            CDSs (total)                      :: 5,483
            Genes (coding)                    :: 5,345
            CDSs (with protein)               :: 5,345
            Genes (RNA)                       :: 119
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 11
            Pseudo Genes (total)              :: 138
            CDSs (without protein)            :: 138
            Pseudo Genes (ambiguous residues) :: 0 of 138
            Pseudo Genes (frameshifted)       :: 32 of 138
            Pseudo Genes (incomplete)         :: 99 of 138
            Pseudo Genes (internal stop)      :: 23 of 138
            Pseudo Genes (multiple problems)  :: 15 of 138
            Pseudo Genes (short protein)      :: 1 of 138
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP110781.1.
            Bacteria and source DNA available from Gian Maria Rossolini.
            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..3576
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="Cf-Emp"
                     /isolation_source="Rectal swab"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="pCf-unmd7"
                     /geo_loc_name="Italy: Empoli"
                     /lat_lon="43.72219201 N 10.93384477 E"
                     /collection_date="2020-01"
                     /collected_by="San Giuseppe Hospital, Empoli, Italy"
     gene            190..321
                     /locus_tag="OPR78_RS27995"
                     /old_locus_tag="OPR78_27980"
     CDS             190..321
                     /locus_tag="OPR78_RS27995"
                     /old_locus_tag="OPR78_27980"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001422066.1"
                     /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_072052181.1"
                     /translation="MHEPPVQSNRCALSGNYRLESNPKRHDKTPLAAATGNGMYKIN"
                     /name="replication initiation protein"
     gene            complement(631..1569)
                     /locus_tag="OPR78_RS28000"
                     /old_locus_tag="OPR78_27985"
     CDS             complement(631..1569)
                     /locus_tag="OPR78_RS28000"
                     /old_locus_tag="OPR78_27985"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_013185833.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_200002678.1"
                     /translation="MSVLDFLSSGGMASIGGDLSEEEQKHTNEIVKLFAKKLREYARTL
                     QIPASNIKINKCSFLFVAKDDFSYHFVFADKPGGGNNLVYRNLSEYRQLELQSIVHQVR
                     IDVGDVVWAFSCPVSLSGEELDTYINKLSIEYIQSEIQSSKDNNDGRISEEAMNVPEIA
                     SGLEKFRKDYPKGKKTAFIIMQFGSTAAHVKLVDAIKKELSKHNIIALRADDKEYMDDL
                     FSNIKTYMYGCDFGIAIFERITEDNFNPNVSLEVGYMMGMGKQVLLLKDKTLSSLHTDL
                     AGKLYKPFDVFDIESSLSTHIGKWLSDKGFL"
                     /name="hypothetical protein"
     gene            complement(2726..3157)
                     /locus_tag="OPR78_RS28005"
                     /old_locus_tag="OPR78_27990"
     CDS             complement(2726..3157)
                     /locus_tag="OPR78_RS28005"
                     /old_locus_tag="OPR78_27990"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000135004.1"
                     /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 domain-containing protein"
                     /protein_id="WP_044703046.1"
                     /translation="MARVSISEAARLVSVSRPTIYKLLKSGELSYTSVVKHGKPVKTID
                     TAELIRLFGALDVVSGDKSDTVKFDGVTTSVNSDFLHSLQHQVALLQAENTGLKDAVNA
                     RDEHISSLRQAMQLLEHKQSTSDPQNVPAKSWWQFWKSH"
                     /name="helix-turn-helix domain-containing protein"
     gene            complement(3160..3348)
                     /locus_tag="OPR78_RS28010"
                     /old_locus_tag="OPR78_27995"
     CDS             complement(3160..3348)
                     /locus_tag="OPR78_RS28010"
                     /old_locus_tag="OPR78_27995"
                     /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_044703047.1"
                     /translation="MTKQQKTALNMAKFIQAQSLFLLGNLNEQDLDTEAGLCEKLHEDA
                     ELLFRTLDIRLDDFQED"
                     /name="Rop family plasmid primer RNA-binding protein"
     Typing          9..521
                     /name="rep_cluster_2358"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.717"
                     /coverage="99.0"
                     /evalue="6.24e-142"
ORIGIN
        1 caaatcagtg gtggcgaaac ccgacaggac tttaaagata ccaggcgttt ccccctggtg
       61 gctccctcgt gcgctctcct gttcctgcct ttcggtttac cggtgtcatt ccgctgttat
      121 ggccgcggtt ctctcattcc acgcctgaca ctcagttccg ggtaggcagt tcgctccaag
      181 ctggactgta tgcacgaacc ccccgttcag tccaaccgct gcgccttatc cggtaactat
      241 cgtcttgagt ccaacccgaa aagacacgac aaaacgccac tggcagcggc cactggtaat
      301 gggatgtaca agattaactg aatgagagtt cttgaagtcc gagctaaact acggctaaac
      361 tgaaaggaca gattacggtt tcagcggtct tgtacaccct gttaccacgg ttcagaagtt
      421 ccccaacttg ctgaaccctc gaaaaaaccg actccccagt cggttttttc gtttctggaa
      481 caagagacta cgacgagaga cgaaggatct caagaagatc tcatcaatca aacgcgtcaa
      541 gtctcaaatt tgaccatgat tttcgcataa ccccattcga taactaacga tgtcaaacaa
      601 gtaccgcaca tacggtactt gttccggaaa ctataaaaat cccttgtctg atagccattt
      661 cccaatatga gtgctgaggg atgactcaat atcgaaaaca tcaaatggct tataaagttt
      721 acctgctaag tctgtatgta atgaacttag agtcttatcc tttaaaagta aaacctgctt
      781 ccccattccc atcatatatc caacttccaa tgaaacatta gggttaaaat tatcttctgt
      841 aatcctctca aaaatagcaa taccgaaatc gcacccatac atatatgttt tgatatttga
      901 aaagagatca tccatatact ctttatcatc agcccttaaa gctattatgt tgtgtttaga
      961 caactctttc tttattgcat caacaagctt tacgtgcgct gccgtgctac caaactgcat
     1021 gatgataaat gctgtttttt tcccttttgg atagtctttt ctgaattttt caaggccaga
     1081 agctatttca gggacattca tagcctcttc tgaaattcta ccatcattgt tatctttact
     1141 actttgaatt tcagactgaa tatattcaat agagagttta ttaatatatg tatcaagttc
     1201 ttccccggag agagagactg ggcaagagaa cgcccaaaca acatcaccaa catcaatccg
     1261 aacctgatgg acgatacttt gaagttcaag ctgtctatat tcagataagt ttctatatac
     1321 taaattatta ccgccaccag gtttatcagc aaacacgaaa tgataagaaa aatcgtcttt
     1381 tgcgacaaac aaaaatgaac atttatttat tttgatattg gatgctggaa tttgtaatgt
     1441 cctagcatac tctctcaatt ttttggcaaa taatttaact atttcattag tatgtttttg
     1501 ttcttcttca gacagatctc caccaatact agccatccca ccggaagata aaaaatccaa
     1561 aacagacata gttaatttcc tttttccaat tctaaagaac gcttggcccg gacatcccaa
     1621 aacctaacca ctacttaatg gtaacatcac ctattcactt gataatgata caacccacct
     1681 tgagtctact gccatctatt taacataagc actcattacg cgcatcgctc agacgcactc
     1741 tgagcgcttt tggggtgagt gcgtcgtttt gtacagttta cccgggggaa aacgctcaga
     1801 acgccacaga tgaatcctga gagggtgaat aactatgctc ccggctgcat ggtgcgtgat
     1861 ttgacggaaa acagccgcta aaagggagat ttttcccggt ttactagccc gggaatccgg
     1921 gattgatgaa gcctatttgt tccgtcccat accatagggg gtcagtttcc cgtccctgat
     1981 ttgcaaagcg ccccgtgcta acttcccggc cacggaagaa cggtgcatct catcatgtct
     2041 ccgtcggttc tcctgagccg tcatcggcct gatctccaga tccgaaaact ctctcttaaa
     2101 ctccgccccc agaaatttca ggtcatcgat aagggtcgca aaccattctt tcaccttttt
     2161 acctccacac tagtaagcca ttcagataac agtctggcac agactggcta aagaaagcgg
     2221 tgaacgggca cgcaatttat tgcggggtcg tgaggcgctg gcagggtgtc ggggcgcatc
     2281 catgacaggt cttttatcta taacaccgcg cagggagaga tactgatatc gcaccacaca
     2341 aacagaaaaa gggtatacca agtgcaatcc cttatcctgt gtggcactga agccctcaga
     2401 gcagcttttc aggtatacca agccagttac cacctggtat accccctaca ggtcttgcca
     2461 gaactggctt taaccgcata aaaacagatg cgggtatacc atttcataca aggggtggta
     2521 tacccccgga agccttgtca gcaaaggctt ccggcattag ccgtgtatac tgcgtggggt
     2581 gtgacacgat tttttggcct ttatcagcca tcagaaatca aacatgcggg taaagcggtc
     2641 agatgagaaa gtataaacat ccatatccgg tgatagcctg gtggctggcc gaacgctatg
     2701 accggaatgc atgattgata atgactcaat gggatttcca gaactgccac caggactttg
     2761 caggaacatt ctgcgggtca gaagtactct gtttatgctc cagaagttgc atggcctgac
     2821 gaagtgaact tatatgctca tcccgtgcat tcactgcatc tttaagcccg gtattctccg
     2881 cctgtaaaag cgccacttga tgctgtaaag aatgtaaaaa atcactgtta accgacgtag
     2941 tgacaccgtc aaattttaca gtgtcacttt tatcaccact gacaacatca agagcaccaa
     3001 aaagacgaat aagctcagct gtatcaatgg ttttaacggg ttttccatgc tttacaacgg
     3061 aggtgtagct aagctcacca gatttaagca gcttgtaaat agtcgggcga ctgacactga
     3121 caagacgtgc agcttcacta atggatacgc gagccattac taatcctctt gaaaatcatc
     3181 cagacgaata tccagagtac gaaaaagcag ttccgcatcc tcatgcaatt tttcgcacaa
     3241 gccggcttca gtatcgagat cctgttcatt gagattaccc agcaagaaca gggattgcgc
     3301 ctgaatgaat ttcgccatat tcagtgccgt tttctgttgt ttcgtcatca cagtgtcagt
     3361 gctccaaatg atatccggtt cttttccgct tcctcgaccg ttcgctcgct acgctcggtc
     3421 acttatctgc ggcgagcgga cgcatcttcc taagagacaa ataacgtaga cggtaagcgt
     3481 aacgaaaagc cagaacaaga acgataaagc catgcccgac cagggcgttt ttccataggc
     3541 ttcgcccccc tgacaagcat cacaaaattt gacgct
//
