LOCUS       NZ_CP011652             3223 bp    DNA     circular CON 31-MAR-2024
DEFINITION  Citrobacter freundii strain CAV1741 plasmid pCAV1741-3223, complete
            sequence.
ACCESSION   NZ_CP011652
VERSION     NZ_CP011652.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN03733754
            Assembly: GCF_001022275.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter freundii
  ORGANISM  Citrobacter freundii
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 3223)
  AUTHORS   Sheppard,A.E., Stoesser,N., Wilson,D., Sebra,R., Kasarskis,A.,
            Anson,L., Giess,A., Pankhurst,L., Vaughan,A., Grim,C.J., Cox,H.,
            Yeh,A., Sifri,C.D., Walker,S., Peto,T.E., Crook,D.W. and
            Mathers,A.J.
  TITLE     Rapid spread of a carbapenem resistance gene driven by multiple
            levels of genetic mobility
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3223)
  AUTHORS   Sheppard,A.E., Stoesser,N., Wilson,D., Sebra,R., Kasarskis,A.,
            Anson,L., Giess,A., Pankhurst,L., Vaughan,A., Grim,C.J., Cox,H.,
            Yeh,A., Sifri,C.D., Walker,S., Peto,T.E., Crook,D.W. and
            Mathers,A.J.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-JUN-2015) University of Oxford, John Radcliffe
            Hospital, Oxford OX39DU, United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: HGAP3 v. 2.2.0
            Genome Coverage                   :: 47X
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_001022275.1-RS_2024_03_31
            Annotation Date                   :: 03/31/2024 01:56:02
            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)                     :: 5,287
            CDSs (total)                      :: 5,166
            Genes (coding)                    :: 5,044
            CDSs (with protein)               :: 5,044
            Genes (RNA)                       :: 121
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 122
            CDSs (without protein)            :: 122
            Pseudo Genes (ambiguous residues) :: 0 of 122
            Pseudo Genes (frameshifted)       :: 33 of 122
            Pseudo Genes (incomplete)         :: 81 of 122
            Pseudo Genes (internal stop)      :: 22 of 122
            Pseudo Genes (multiple problems)  :: 14 of 122
            Pseudo Genes (short protein)      :: 1 of 122
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP011652.1.
            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..3223
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="CAV1741"
                     /isolation_source="Respiratory"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="pCAV1741-3223"
                     /geo_loc_name="USA:Virginia"
                     /lat_lon="38.14 N 78.45 W"
                     /collection_date="2012-10"
                     /collected_by="Clinical Microbiology University of Virginia
                     Health System"
     gene            126..341
                     /locus_tag="AB183_RS27890"
     CDS             126..341
                     /locus_tag="AB183_RS27890"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137421.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_024195375.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLIQRENA
                     ALNERVTVLSRQVQSLSEQLRRLSKG"
                     /name="MbeD family mobilization/exclusion protein"
     gene            509..841
                     /locus_tag="AB183_RS00020"
                     /old_locus_tag="AB183_00020"
     CDS             509..841
                     /locus_tag="AB183_RS00020"
                     /old_locus_tag="AB183_00020"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008784643.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="EmrE family multidrug efflux SMR transporter"
                     /protein_id="WP_001099531.1"
                     /translation="MNTYIFLGGAIVAEVIGTTFMKYSEGFTRLWPSVGTAISYCAAFY
                     LLSQTLENIPTGIAYAIWSGAGIVLISLAGWLVSGQKLDWPAIAGMFLICVGVLVINIF
                     SKSSAH"
                     /name="EmrE family multidrug efflux SMR transporter"
     gene            complement(1050..1220)
                     /locus_tag="AB183_RS00025"
                     /old_locus_tag="AB183_00025"
     CDS             complement(1050..1220)
                     /locus_tag="AB183_RS00025"
                     /old_locus_tag="AB183_00025"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_005761324.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004193911.1"
                     /translation="MHEPPVQSDYHARSGNYQLESNPERHDKSPVAVAIGNWVHGAEIV
                     ENAYRVLEVKA"
                     /name="hypothetical protein"
     gene            1859..2182
                     /locus_tag="AB183_RS00030"
                     /old_locus_tag="AB183_00030"
     CDS             1859..2182
                     /locus_tag="AB183_RS00030"
                     /old_locus_tag="AB183_00030"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000957083.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_004193914.1"
                     /translation="MLTMWVTEDEHRRLLERCEGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQIVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2391..>2825
                     /locus_tag="AB183_RS28355"
                     /pseudo=""
     CDS             2391..>2825
                     /locus_tag="AB183_RS28355"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /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="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     ARG             510..841
                     /name="qacG"
                     /gene="qacG"
                     /gene_name="small multidrug resistance (SMR) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="disinfecting agents and antiseptics"
                     /identity="41.35"
                     /coverage="102.8"
     Typing          1572..1763
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.308"
                     /coverage="89.0"
                     /evalue="3.38e-71"
     Typing          complement(1109..1589)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.867"
                     /coverage="93.0"
                     /evalue="1.73e-132"
     Typing          3..439
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="85.811"
                     /coverage="99.0"
                     /evalue="2.7299999999999998e-67"
     Typing          2173..3221
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="94.286"
                     /coverage="99.0"
                     /evalue="0.0"
ORIGIN
        1 agaggaacag cggcgtacag ctctcgacct gcggcgagca gagacgccgc tgcgtgaggg
       61 tgaacccgga agcgggacag ttcggagagg actcgagctg gatgatactg gcggggaaat
      121 agcacatgac ggagctggaa aaacagttgc tgagcgcatt agagcagcta cagcaggact
      181 actcgaaaag gctggacgag tgggagaacg ccttcgcgga atggcggacg atgtctggtc
      241 ttattcaacg ggagaacgcg gcgctgaacg agcgcgtcac ggtcttgagc aggcaggtgc
      301 agagtttgag cgagcagctg cgccggttgt cgaaaggctg aacgcgatag aaactcaccg
      361 gcagcaggag cgggcggtgc agcaccagaa agcgctggag ctggaacgat cgcagtggca
      421 gcatcatggt ccttcgctat gataagccgg gttctattaa ttagttgtta tgtaaagata
      481 tttaaatttt tcaacatgag gtatttttat gaatacatat attttcctgg gaggggctat
      541 tgtggctgaa gtcataggca ccacctttat gaaatattca gaaggattta cacgcctgtg
      601 gccgtctgta ggaactgcaa taagttattg cgctgccttt tatctgcttt cccaaacatt
      661 ggaaaatata cctaccggta ttgcttacgc aatttggtct ggtgcgggaa ttgtactaat
      721 aagcctagct ggttggttgg ttagcggtca aaaacttgat tggcccgcaa ttgcaggaat
      781 gttccttatt tgcgttggag ttttggttat taatattttt tcaaaatctt ctgcgcatta
      841 actttttacc gaagcatatt ggccaaagca aaaggatttc cttgagatcc tttctttctg
      901 cgcgtaatct ttttccctgt aaacaaaaaa accaccgcta ccaacggtgg ttcgtttgcc
      961 ggaattcaga gctaccaact ctttgttccg atggtaactg gctttcacgg agcgcagata
     1021 cctaaactgt cctttcagtg tagccgcact caggctttca cttcaagaac tctgtaggca
     1081 ttctctacaa tctctgctcc gtgaacccag ttaccaatgg ctaccgccac tggcgatttg
     1141 tcgtgtcttt ccgggttgga ctcaagttga tagttaccgg aacgggcgtg gtagtcggac
     1201 tgaacggggg gttcgtgcat acagtccatc ctggagcgaa ctgcctaccc ggaaccgagt
     1261 ttcaggcgtg gaatgagaaa ccgcggccat aacagcggaa tgacaccggt aaaccgaaag
     1321 gcaggaatgc gggggagcac gagggagcca ccagggggaa acgcctggta tctttaagcc
     1381 gcatcgggtt tcgccaccgc tgatttgagc gtcattttcg tgatactcgt caggggggcg
     1441 gagcctatgg aaaaacggca actccgcatc cttttcttgg cctttcctgc ttcgagcggc
     1501 atttgcttat cccgtaatct gtgagctggt aacgcccgcc gcagtctcac ggcaggagcg
     1561 tagcgaccga gtgagcgagg aggcgtcatt tcatcaccac ctgcattttg cacttacgcc
     1621 cggcagccgc atttttcccc tgtcacatga agcactttca taaattgcca ctccgtcata
     1681 acatgtttag ccagtataca ctccgctagc gctacgtgac tggttcaggg ctgcgccccg
     1741 aaacccgcta aaaccactgc cgcgcctgcg gcttgtccaa caccgtgccg accgggaaaa
     1801 gatttcccgt ccgtcccggc gttatcagga ggccggattg gcagacaaac gcagcaaaat
     1861 gctcaccatg tgggtgactg aggacgagca ccggcgtctg ctggagcgct gcgagggtaa
     1921 gcaactcgcg gcctggatgc ggcagacgtg cctggacgag aagcccgcac gcgccggcaa
     1981 acttccgtcg atctcgccgg cgctgcttcg tcagcttgcc ggcatgggga acaaccttaa
     2041 ccagattgcc cgccaggtta acgccggtgg tggaagcgga cacgaccgcg tgcagattgt
     2101 cgccgcgctg atggccatcg atgccggact cgagcggttg cggcatgccg tactggaaaa
     2161 gggtgctgat gatgatcgtt aagtttcatc ctcgggggcg cggcggcggc ggcgggccgg
     2221 tcgattatct gctgggtaaa gatcgccagc gcgacggcgc cagcgttctg caggggaagc
     2281 cggatgaagt ccgggagctt atcgacgcct cgccctacgc caaaaagtac acttccggcg
     2341 ttctgtcttt tgccgaacag gatttaccgc ccggccagcg cgaaaagctg atggcgagtt
     2401 tcgagcgggt tctgatgccc ggactcgata aagaccagta cagcgtgctg tgggttgagc
     2461 accgggacaa ggggcggctg gagctgaact tcctgatccc gaacacggag cttctgaccg
     2521 gcaagcggct acagccgtat tacgaccgcg ccgaccgtcc gcgcatcgat gcctggcaga
     2581 ccatagtgaa cggcaggctg gggctgcatg acccgaacgc gccggagaac cggcgggtgc
     2641 tggtctcgcc ttccgcgctg ccggaagcga agcaggaagc cgcccaggcg attacgagcg
     2701 gcctgcttgc ccttgcctca tccggggagc tgaaaacgcg tcaggacgtc actgaggcgc
     2761 tggaaagcgc aggttttgag gtggtgcgca ccacaaaaag cagcatcagc attgccgacc
     2821 cggacggggg gcgaaacatc cgactgaagg gagccatcta tgaacagtct tttaacgctg
     2881 gcgaaggact tagagcagaa atcgaaagcg cagcagcaga ctaccggcga gatgctgaaa
     2941 gccgcattca gcgagcacga gaagtctgtc agagcggaac tgagcgaaag cgagaagaga
     3001 atcagcgccg ccatcctcga ccacgaccgg aagctgtcct cagccatgag ccagcgcacg
     3061 aaagggatgc tgcgcatggt cagccagacg tggctgacca tcgttctggt ctccgcgctg
     3121 ctgatagcgt cgagcgcggg cattctgtgg tggcaggggc agcagatact cgagaactat
     3181 acgaccatcc gggagcagaa gagcacgcag gccatgctgt cag
//
