LOCUS       NZ_CP011605             3820 bp    DNA     circular CON 31-MAR-2024
DEFINITION  Citrobacter freundii strain CAV1321 plasmid pCAV1321-3820, complete
            sequence.
ACCESSION   NZ_CP011605
VERSION     NZ_CP011605.1
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 3820)
  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  JOURNAL   Unpublished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 3820)
  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
            CP011605.1.
            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..3820
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="CAV1321"
                     /isolation_source="Urine/Genitourinary"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="pCAV1321-3820"
                     /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            complement(444..576)
                     /locus_tag="AB180_RS29295"
                     /pseudo=""
     CDS             complement(444..576)
                     /locus_tag="AB180_RS29295"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="frameshifted; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="replication initiation protein"
                     /name="replication initiation protein"
     gene            1224..1547
                     /locus_tag="AB180_RS00035"
                     /old_locus_tag="AB180_00035"
     CDS             1224..1547
                     /locus_tag="AB180_RS00035"
                     /old_locus_tag="AB180_00035"
                     /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_024262785.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGVD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1756..>2190
                     /locus_tag="AB180_RS28965"
                     /pseudo=""
     CDS             1756..>2190
                     /locus_tag="AB180_RS28965"
                     /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            2225..2722
                     /locus_tag="AB180_RS28490"
     CDS             2225..2722
                     /locus_tag="AB180_RS28490"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001086853.1"
                     /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_128350943.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQTTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMLRMVSQTWLTIVLVSTLLIASSAGILWWQGQQIL
                     DNYTSIREQKDALEKLNARTWGVRYQEDSQGRFLVLPEGVKADTNWTFDNGRKKGIRLV
                     QE"
                     /name="MbeB family mobilization protein"
     gene            2729..2944
                     /locus_tag="AB180_RS28495"
     CDS             2729..2944
                     /locus_tag="AB180_RS28495"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137422.1"
                     /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_032333604.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALNERVTGLSRQVQSLSEQLRRLSNS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            3231..3479
                     /locus_tag="AB180_RS00045"
                     /old_locus_tag="AB180_00045"
     CDS             3231..3479
                     /locus_tag="AB180_RS00045"
                     /old_locus_tag="AB180_00045"
                     /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_023063530.1"
                     /translation="MGRKKNQLGTQIHQLKKSNDKIFSALASTASRLDAVERVQADADM
                     RVRNLEIKMKSMSGAKNKDIAVEYDLSEGRVSQIINQ"
                     /name="hypothetical protein"
     gene            3491..3790
                     /locus_tag="AB180_RS00050"
                     /old_locus_tag="AB180_00050"
     CDS             3491..3790
                     /locus_tag="AB180_RS00050"
                     /old_locus_tag="AB180_00050"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006524481.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="virulence factor"
                     /protein_id="WP_024262786.1"
                     /translation="MYAIAFDLDQDMLEQTYHVPSYQNAYGDIKKALEAHGFTRQQGSV
                     YFGDVSKVDAVSCVLAVMDLAKKNPWFAPSVQDIRMLRIEENNDLMPAVRKAVE"
                     /name="virulence factor"
     Typing          938..1110
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="98.276"
                     /coverage="100.0"
                     /evalue="9.21e-81"
     Typing          complement(412..1013)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="91.817"
                     /coverage="99.0"
                     /evalue="0.0"
     Typing          1538..3039
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 tgggggtatt tatgagtgag atgtcatctg gtgaaataag tcttccacat gtttgtccat
       61 gtgcaaaata tgagtgcgct caattcccaa caactgctaa ctcatttcaa gagttatatg
      121 cattgtttgg tttcagaaat atggatgacg cgatgagaaa tcagagttgg tgtaaatcgt
      181 gtcgtgctaa agataatgca gagagaagag ctagaaaatc ttcaagttga ggatcaaata
      241 acacttgtta ttgagatcat tcgtttctga gcgtaatctc ctaagccgta aacaaaaaaa
      301 ccaccgctac caacggtggt tagtttgccg gaattcagag ctaccaactc tttattccga
      361 aggtaactgg gtgtacgaga ccacagatac caaatactgt cctttcagtg tagccgcagt
      421 caggccacca cttcaagaac tctctaaata tctctcgtac acaagttacc aatggctgct
      481 gccagtggcg ctttgtcgtg cctttttcgg attggactca agacgatagt taccgaataa
      541 ggcgcagcag tcggactgaa cggggggttc gtgcatacag tccagcttgg agcgaactgc
      601 cttcccggaa ccgagtgtca ggcgtggaat gagataaacg cggccataac agcggattga
      661 catcggtaaa ccgaaaggca ggaacaggag agcgcacgag ggagccacca gggggaaacg
      721 cctggtatct ttaagtcctg tcgggtttcg ccaccactga tttgagcgtc agatttcgtg
      781 atgcttgtca ggggggcgga gcctatggaa aaacggcttc gccgtggcct tatcgcttcc
      841 ctgttaagct tcttcctggc atctcccagg aaatttccgc cccgcctgta agtcggtacc
      901 gctcgccgca gccgaacgac cgagcgcagc gagtcagtga gcgaggaagc ggaatatatc
      961 ctgtatcaca tattctgctg acgctccgct gctgcatttt tctcctgcca catgaagcac
     1021 ttcactgaca ctcgcatccg tgccaacata gtaagccagt atacactccg ctagcgctac
     1081 gtgactggtt cagggctgcg ccccgaaacc tgctaaaacc actgacgcgc ctgcggcttg
     1141 tccaacaccg cgtcgatcgg gaaaagattt cccgcccgtc ccggcgttat caggaggccg
     1201 gattggcaga taaacgcagc aaaatgctca ctatgtgggt gaccgaggat gagcaccggc
     1261 gtctgctgga gcgctgcgac ggtaaacagc tcgcggcctg gatgcgtcag acgtgtctgg
     1321 acgagaagcc cgcccgcgcc ggcaaacttc cctcgatctc gccggcgctg cttcgtcagc
     1381 ttgccggcat gggtaacaac ctcaaccaga ttgcccggca ggttaacgcc ggtggcggca
     1441 gcggacacga ccgtgtgcag gttgttgccg cgctgatggc catcgatgcc ggacttgaac
     1501 gcctgcggca cgccgtgctg gaaaaggggg tagacgatga tcgttaagtt tcatccgcga
     1561 gggcgcggcg gtggtgccgg tccggtggat tatctgctgg gcaaagaccg gcagcgcgac
     1621 ggcgccagta tcctgcaggg gaagccggag gaagtccggg agcttatcga cgcctcgccc
     1681 tacgcaaaaa aatatacctc cggcgtcctg tcctttgccg aacaggactt accgcccggg
     1741 cagcgtgaaa agctgatggc gagcttcgag cgggttctga tgcccggact cgataaagac
     1801 cagtacagcg tgctgtgggt tgagcaccag gacaaggggc ggctggagct gaacttcctg
     1861 atcccgaaca cggagctgct gaccggcaaa cggctccagc cgtattacga ccgcgccgac
     1921 cgtccgcgca tcgatgcctg gcagaccatt gtgaacggca ggctggggct gcacgacccg
     1981 aacgcaccgg agaaccggcg ggcgctggtc acgccgtccg cgctgccgga aacaaagcag
     2041 gaagccgctc aggcaattac gcggggttta ctctccttag cgtcgtccgg ggagcttaaa
     2101 acgcgtcagg acgtcactaa ggcgctggaa agtgcaggtt ttgaggtggt gcgcaccacg
     2161 aaaagcagca tcagtattgc cgacccggac ggggggcgaa acatccgact gaagggagcc
     2221 atctatgaac agtcttttaa cgctggcgaa ggacttagag cagaaatcga aagcgcagca
     2281 gcagactacc ggcgagatgc tgaaagccgc attcagcgag cacgagaagt ctgtcagagc
     2341 ggaactgagc gaaagcgaga agagaatcag cgccgccatc ctcgaccacg accggaagct
     2401 gtcctcagcc atgagccagc gcacgaaagg gatgctgcgc atggtcagcc agacgtggct
     2461 gaccatcgtc ctggtgtcca cgctgctgat agcctcgagc gcgggcattc tgtggtggca
     2521 ggggcaacag atactcgaca attacacgag tatccgggag cagaaagacg cgctggagaa
     2581 gctgaacgcc aggacgtggg gcgtgaggta ccaggaagac agccaggggc gttttctggt
     2641 gctgccggag ggcgtgaaag cggacacgaa ctggacgttc gacaacggca ggaagaaggg
     2701 catcagactg gtacaggagt agagcagcat gacggagctg gaaaaacagt tattgagcgc
     2761 attagagcag ctacaacagg actactcgaa aaggctggac gagtgggaga atgccttcgc
     2821 ggaatggcgg acgatgtctg gacttatgca acgggagaac gcggcgctga acgagcgcgt
     2881 cacgggcttg agcaggcagg tgcagagttt gagcgagcag ctgcgccggt tgtcgaacag
     2941 ttgaatacaa tcgaacatcg ccagcagcat gaacggagcc aggtccagaa aatactggag
     3001 ctagaaaaag caccgagagc tagatatggg ccaactcttt aagtgactgt atttattggt
     3061 aaatcttgcc tttagctaaa taaaatacat gacaactaaa gttttttttt atatattgtt
     3121 gattttattc gtttttattt ttagttcttt aattgatgtg cttttttgtt gaaatttatg
     3181 tttgttgttg tattgtcgtt ggcaactata gcaatcttaa tggtgcaaag atggggcgta
     3241 aaaaaaacca actgggaact cagattcatc agttaaagaa aagtaacgac aagatctttt
     3301 ccgctttagc aagtacggca tcgcgtcttg atgctgttga gcgagttcaa gctgatgccg
     3361 atatgagagt taggaatctt gagataaaga tgaagtctat gtctggtgcc aaaaataaag
     3421 atattgccgt tgagtatgat ctgtctgaag gtcgcgtctc tcaaattata aatcagtagg
     3481 aataattatt atgtacgcta tagcgtttga tcttgatcag gatatgttag agcaaacata
     3541 ccatgtacct agttatcaga atgcttatgg agacatcaag aaggctctag aagcacatgg
     3601 cttcacaaga cagcaaggaa gtgtatattt tggggatgta tctaaagtcg atgctgtttc
     3661 ttgtgttttg gctgtaatgg atttggcaaa aaaaaatccg tggttcgctc catctgttca
     3721 agatattagg atgttgagga ttgaggaaaa taacgatctt atgccagccg ttcgtaaggc
     3781 agtggaataa actttaaatt ttgcacatta ataatatgtc
//
