LOCUS       NZ_CP011604             3223 bp    DNA     circular CON 31-MAR-2024
DEFINITION  Citrobacter freundii strain CAV1321 plasmid pCAV1321-3223, complete
            sequence.
ACCESSION   NZ_CP011604
VERSION     NZ_CP011604.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN03733741
            Assembly: GCF_001022155.1
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  JOURNAL   Unpublished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. 2.3.0
            Genome Coverage                   :: 115X
            Sequencing Technology             :: PacBio
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_001022155.1-RS_2024_03_31
            Annotation Date                   :: 03/31/2024 02:09:54
            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)                     :: 5,394
            CDSs (total)                      :: 5,273
            Genes (coding)                    :: 5,156
            CDSs (with protein)               :: 5,156
            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)              :: 117
            CDSs (without protein)            :: 117
            Pseudo Genes (ambiguous residues) :: 0 of 117
            Pseudo Genes (frameshifted)       :: 29 of 117
            Pseudo Genes (incomplete)         :: 83 of 117
            Pseudo Genes (internal stop)      :: 19 of 117
            Pseudo Genes (multiple problems)  :: 14 of 117
            Pseudo Genes (short protein)      :: 1 of 117
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP011604.1.
            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="CAV1321"
                     /isolation_source="Urine/Genitourinary"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="pCAV1321-3223"
                     /geo_loc_name="USA:Virginia"
                     /lat_lon="38.14 N 78.45 W"
                     /collection_date="2010-11"
                     /collected_by="Clinical Microbiology University of Virginia
                     Health System"
     gene            join(3000..3223,1..109)
                     /locus_tag="AB180_RS00015"
                     /old_locus_tag="AB180_00015"
     CDS             join(3000..3223,1..109)
                     /locus_tag="AB180_RS00015"
                     /old_locus_tag="AB180_00015"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016234454.1"
                     /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(318..488)
                     /locus_tag="AB180_RS00020"
                     /old_locus_tag="AB180_00020"
     CDS             complement(318..488)
                     /locus_tag="AB180_RS00020"
                     /old_locus_tag="AB180_00020"
                     /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            1127..1450
                     /locus_tag="AB180_RS00025"
                     /old_locus_tag="AB180_00025"
     CDS             1127..1450
                     /locus_tag="AB180_RS00025"
                     /old_locus_tag="AB180_00025"
                     /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            1659..>2093
                     /locus_tag="AB180_RS28960"
                     /pseudo=""
     CDS             1659..>2093
                     /locus_tag="AB180_RS28960"
                     /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"
     gene            2128..2613
                     /locus_tag="AB180_RS28475"
     CDS             2128..2613
                     /locus_tag="AB180_RS28475"
                     /inference="COORDINATES: protein motif:HMM:NF016710.4"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_025367738.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSALLIASSAGILWWQGQQIL
                     ENYTTIREQKSTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGQFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            2617..2832
                     /locus_tag="AB180_RS28480"
     CDS             2617..2832
                     /locus_tag="AB180_RS28480"
                     /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"
     ARG             3001..3221
                     /name="qacJ"
                     /gene="qacJ"
                     /gene_name="small multidrug resistance (SMR) antibiotic
                     efflux pump"
                     /tool="rgi"
                     /drug_class="disinfecting agents and antiseptics"
                     /identity="47.89"
                     /coverage="69.16"
     Typing          840..1031
                     /name="MOB_unknown"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="92.308"
                     /coverage="89.0"
                     /evalue="3.38e-71"
     Typing          complement(377..857)
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="84.867"
                     /coverage="93.0"
                     /evalue="1.73e-132"
     Typing          1441..2930
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="91.784"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ttggttggtt agcggtcaaa aacttgattg gcccgcaatt gcaggaatgt tccttatttg
       61 cgttggagtt ttggttatta atattttttc aaaatcttct gcgcattaac tttttaccga
      121 agcatattgg ccaaagcaaa aggatttcct tgagatcctt tctttctgcg cgtaatcttt
      181 ttccctgtaa acaaaaaaac caccgctacc aacggtggtt cgtttgccgg aattcagagc
      241 taccaactct ttgttccgat ggtaactggc tttcacggag cgcagatacc taaactgtcc
      301 tttcagtgta gccgcactca ggctttcact tcaagaactc tgtaggcatt ctctacaatc
      361 tctgctccgt gaacccagtt accaatggct accgccactg gcgatttgtc gtgtctttcc
      421 gggttggact caagttgata gttaccggaa cgggcgtggt agtcggactg aacggggggt
      481 tcgtgcatac agtccatcct ggagcgaact gcctacccgg aaccgagttt caggcgtgga
      541 atgagaaacc gcggccataa cagcggaatg acaccggtaa accgaaaggc aggaatgcgg
      601 gggagcacga gggagccacc agggggaaac gcctggtatc tttaagccgc atcgggtttc
      661 gccaccgctg atttgagcgt cattttcgtg atactcgtca ggggggcgga gcctatggaa
      721 aaacggcaac tccgcatcct tttcttggcc tttcctgctt cgagcggcat ttgcttatcc
      781 cgtaatctgt gagctggtaa cgcccgccgc agtctcacgg caggagcgta gcgaccgagt
      841 gagcgaggag gcgtcatttc atcaccacct gcattttgca cttacgcccg gcagccgcat
      901 ttttcccctg tcacatgaag cactttcata aattgccact ccgtcataac atgtttagcc
      961 agtatacact ccgctagcgc tacgtgactg gttcagggct gcgccccgaa acccgctaaa
     1021 accactgccg cgcctgcggc ttgtccaaca ccgtgccgac cgggaaaaga tttcccgtcc
     1081 gtcccggcgt tatcaggagg ccggattggc agacaaacgc agcaaaatgc tcaccatgtg
     1141 ggtgactgag gacgagcacc ggcgtctgct ggagcgctgc gagggtaagc aactcgcggc
     1201 ctggatgcgg cagacgtgcc tggacgagaa gcccgcacgc gccggcaaac ttccgtcgat
     1261 ctcgccggcg ctgcttcgtc agcttgccgg catggggaac aaccttaacc agattgcccg
     1321 ccaggttaac gccggtggtg gaagcggaca cgaccgcgtg cagattgtcg ccgcgctgat
     1381 ggccatcgat gccggactcg agcggttgcg gcatgccgta ctggaaaagg gtgctgatga
     1441 tgatcgttaa gtttcatcct cgggggcgcg gcggcggcgg cgggccggtc gattatctgc
     1501 tgggtaaaga tcgccagcgc gacggcgcca gcgttctgca ggggaagccg gatgaagtcc
     1561 gggagcttat cgacgcctcg ccctacgcca aaaagtacac ttccggcgtt ctgtcttttg
     1621 ccgaacagga tttaccgccc ggccagcgcg aaaagctgat ggcgagtttc gagcgggttc
     1681 tgatgcccgg actcgataaa gaccagtaca gcgtgctgtg ggttgagcac cgggacaagg
     1741 ggcggctgga gctgaacttc ctgatcccga acacggagct tctgaccggc aagcggctac
     1801 agccgtatta cgaccgcgcc gaccgtccgc gcatcgatgc ctggcagacc atagtgaacg
     1861 gcaggctggg gctgcatgac ccgaacgcgc cggagaaccg gcgggtgctg gtctcgcctt
     1921 ccgcgctgcc ggaagcgaag caggaagccg cccaggcgat tacgagcggc ctgcttgccc
     1981 ttgcctcatc cggggagctg aaaacgcgtc aggacgtcac tgaggcgctg gaaagcgcag
     2041 gttttgaggt ggtgcgcacc acaaaaagca gcatcagcat tgccgacccg gacggggggc
     2101 gaaacatccg actgaaggga gccatctatg aacagtcttt taacgctggc gaaggactta
     2161 gagcagaaat cgaaagcgca gcagcagact accggcgaga tgctgaaagc cgcattcagc
     2221 gagcacgaga agtctgtcag agcggaactg agcgaaagcg agaagagaat cagcgccgcc
     2281 atcctcgacc acgaccggaa gctgtcctca gccatgagcc agcgcacgaa agggatgctg
     2341 cgcatggtca gccagacgtg gctgaccatc gttctggtct ccgcgctgct gatagcgtcg
     2401 agcgcgggca ttctgtggtg gcaggggcag cagatactcg agaactatac gaccatccgg
     2461 gagcagaaga gcacgcaggc catgctgtca gagaggaaca gcggcgtaca gctctcgacc
     2521 tgcggcgagc agagacgccg ctgcgtgagg gtgaacccgg aagcgggaca gttcggagag
     2581 gactcgagct ggatgatact ggcggggaaa tagcacatga cggagctgga aaaacagttg
     2641 ctgagcgcat tagagcagct acagcaggac tactcgaaaa ggctggacga gtgggagaac
     2701 gccttcgcgg aatggcggac gatgtctggt cttattcaac gggagaacgc ggcgctgaac
     2761 gagcgcgtca cggtcttgag caggcaggtg cagagtttga gcgagcagct gcgccggttg
     2821 tcgaaaggct gaacgcgata gaaactcacc ggcagcagga gcgggcggtg cagcaccaga
     2881 aagcgctgga gctggaacga tcgcagtggc agcatcatgg tccttcgcta tgataagccg
     2941 ggttctatta attagttgtt atgtaaagat atttaaattt ttcaacatga ggtattttta
     3001 tgaatacata tattttcctg ggaggggcta ttgtggctga agtcataggc accaccttta
     3061 tgaaatattc agaaggattt acacgcctgt ggccgtctgt aggaactgca ataagttatt
     3121 gcgctgcctt ttatctgctt tcccaaacat tggaaaatat acctaccggt attgcttacg
     3181 caatttggtc tggtgcggga attgtactaa taagcctagc tgg
//
