LOCUS       NZ_CP011606             4310 bp    DNA     circular CON 31-MAR-2024
DEFINITION  Citrobacter freundii strain CAV1321 plasmid pCAV1321-4310, complete
            sequence.
ACCESSION   NZ_CP011606
VERSION     NZ_CP011606.1
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 4310)
  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  JOURNAL   Unpublished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 4310)
  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
            CP011606.1.
            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..4310
                     /organism="Citrobacter freundii"
                     /mol_type="genomic DNA"
                     /strain="CAV1321"
                     /isolation_source="Urine/Genitourinary"
                     /host="Homo sapiens"
                     /db_xref="taxon:546"
                     /plasmid="pCAV1321-4310"
                     /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(44..253)
                     /locus_tag="AB180_RS28500"
     CDS             complement(44..253)
                     /locus_tag="AB180_RS28500"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014538403.1"
                     /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_001632067.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWESAFAEWRTMCGLMQRENA
                     ALSERVTDLSTQVLSLSEQLRRLS"
                     /name="MbeD family mobilization/exclusion protein"
     gene            complement(257..742)
                     /locus_tag="AB180_RS28505"
     CDS             complement(257..742)
                     /locus_tag="AB180_RS28505"
                     /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_012782630.1"
                     /translation="MNSLLTLAKDLEQKSKVQQQTTGEMLKAAFSEHEKSVRAELNESE
                     KRISAAIHDHDRMLSSAMSQRTKGMLRMVSQTWLTIVLVSVLLIASSAGILWWQGQQIL
                     DNYTTIREQKSTQAMLSERNSGVQLTTCGEERRRCVRVNPDAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            complement(<777..1481)
                     /locus_tag="AB180_RS29300"
                     /pseudo=""
     CDS             complement(<777..1481)
                     /locus_tag="AB180_RS29300"
                     /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            complement(1420..1743)
                     /locus_tag="AB180_RS00060"
                     /old_locus_tag="AB180_00060"
     CDS             complement(1420..1743)
                     /locus_tag="AB180_RS00060"
                     /old_locus_tag="AB180_00060"
                     /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_001555769.1"
                     /translation="MLTMWVTEDEHRRLLERCDGKQLAAWMRQTCLDEKPARAGKLPSI
                     SPALLRQLAGMGNNLNQIARQVNAGGSSGLDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            2382..2540
                     /locus_tag="AB180_RS29305"
     CDS             2382..2540
                     /locus_tag="AB180_RS29305"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_007772075.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_032670878.1"
                     /translation="MHEPPVQSDCCALSGNYRLESNPERHEKSLLAAAISNWRYTRDKL
                     RGLEVWA"
                     /name="hypothetical protein"
     gene            complement(2777..3046)
                     /locus_tag="AB180_RS00065"
                     /old_locus_tag="AB180_00065"
     CDS             complement(2777..3046)
                     /locus_tag="AB180_RS00065"
                     /old_locus_tag="AB180_00065"
                     /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_079839079.1"
                     /translation="MNGQEFRLLLTEHGEKEAVLLFGKKSFVAVPDTQNLYGGCYYLYL
                     EDAHKNELLIELNESDLYPGGAIELQHNGGRKIHCEILKVRWSR"
                     /name="hypothetical protein"
     gene            3342..3575
                     /locus_tag="AB180_RS00070"
                     /old_locus_tag="AB180_00070"
     CDS             3342..3575
                     /locus_tag="AB180_RS00070"
                     /old_locus_tag="AB180_00070"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_008461706.1"
                     /GO_component="GO:0005886 - plasma membrane [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YgdI/YgdR family lipoprotein"
                     /protein_id="WP_001036746.1"
                     /translation="MNKKTLLAAMMVALVTFAAAGCSSNQEIKTTDDRTIVTDGKPKVD
                     SDTGLVSYKDAHTGRTEQINRDKITNMSELDN"
                     /name="YgdI/YgdR family lipoprotein"
     gene            3597..3824
                     /locus_tag="AB180_RS00075"
                     /old_locus_tag="AB180_00075"
     CDS             3597..3824
                     /locus_tag="AB180_RS00075"
                     /old_locus_tag="AB180_00075"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_010615788.1"
                     /GO_component="GO:0005886 - plasma membrane [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YgdI/YgdR family lipoprotein"
                     /protein_id="WP_000719360.1"
                     /translation="MKKIFVSVFAAAVALSALTGCTRTSYAIHTNDGRTIVSDGKPTES
                     DSGLLGYKDANGVKQQINKADVKEVSEIPH"
                     /name="YgdI/YgdR family lipoprotein"
     Typing          complement(1852..1930)
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="100.0"
                     /coverage="100.0"
                     /evalue="5.8899999999999995e-34"
     Typing          2006..2494
                     /name="ColRNAI_rep_cluster_1987"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="86.747"
                     /coverage="94.0"
                     /evalue="7.82e-151"
     Typing          complement(4..1430)
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="98.95"
                     /coverage="95.0"
                     /evalue="0.0"
ORIGIN
        1 gctgcgcgct cctgctcccg gtgtgcctcg atgtcgttca gccttacgac aaccggcgca
       61 gctgctcgct taaactcagc acctgcgtgc tcaagtccgt gacgcgctcg ctcagcgctg
      121 cgttctcccg ttgcataaga ccacacatcg tccgccattc cgcgaaggcg ctctcccact
      181 cgtccagcct tttcgagtag tcctgctgta gctgctctaa tgcgctcagc aactgttttt
      241 ccagttccgt catgtgctat ttccccgcca gtatcatcca gctcgaatcc tctccgaacc
      301 gtcccgcgtc cgggttcacc ctcacgcagc ggcgtcgttc ctctccgcag gtcgtgagct
      361 gcacgccgct gttcctctcg gacagcatgg cctgcgtgct cttctgctcc cggatggtcg
      421 tgtaattgtc gagtatctgc tgcccctgcc accatagaat gcccgcactt gaggctatca
      481 gcagcacgga gaccaggacg atggtcagcc acgtctggct gaccatgcgc agcatccctt
      541 tcgtacgctg gctcatggct gaggacagca tccggtcgtg gtcgtggatg gcggcgctga
      601 ttctcttctc gctttcgttc agttccgctc tgacagactt ctcgtgctcg ctgaatgcgg
      661 ctttcagcat ctcgccggta gtctgctgct gcactttcga tttctgctct aagtccttcg
      721 ccagcgttaa aagactgttc atagatggct cccttcagtc ggatgtttcg ccccccgtcc
      781 gggtcggcaa tgctgatgct gctttttgtg gtgcgaacca cctcaaaacc tgcgctttcc
      841 agcgcctcag tgacgtcctg acgcgttttc agctccccgg acgaggctaa ggccagtaaa
      901 ccccgcgtaa tcgcctgagc ggcttcctgc ttcgtttccg gcagcgcgga cggcgtgacc
      961 agtgcccgcc ggttttccgg cgcgttcggg tcgtgcagcc ccagactgcc gttcacgatg
     1021 gtctgccagg catcaatgcg aggacggtcg gcgcggtcat agtatggctg gagccgtttg
     1081 ccggtcagca gctccgtgtt cgggatcagg aagttcagct ccagccgccc cttgtcccgg
     1141 tgctcaaccc acagcacgct gtactggtct ttatcgagtc cgggcatcag aacccgctcg
     1201 aagctcgcca tcagcgtttc acgctgcccg ggcggtaagt cctgttcggc aaaggacagc
     1261 accccggagg tgtacttttt ggcgtagggc gaggcgtcga taagctcccg gacttcctcc
     1321 ggcttcccct gaagaacgct ggcaccgtcg cgctggcggt ctttccccag cagataatca
     1381 accgggccgg caccgcctcc gcgtccccgg ggatgaaact taacgatcat cgtcagcccc
     1441 cttttccagt acggcatgcc gcagccgctc gagtccggca tcgatggcca tcagcgcggc
     1501 gacgacctgc acgcggtcga gaccgctact gccaccggcg ttaacctggc gggcaatctg
     1561 gttgaggttg ttccccatgc cggcaagctg acgaagcagc gccggcgaga tcgagggaag
     1621 tttgccggcc cgggcgggct tctcgtccag gcacgtctgc cgcatccagg ccgcgagctg
     1681 tttaccgtcg cagcgttcca gcagacggcg gtgctcatct tctgttaccc acatcgtgag
     1741 cattttgctg cgtttgtctg ccaatccggc ctcctgataa cgccgggacg ggcgggaaat
     1801 cttttcccgg tcggcgcggt gttgggcaag ccgcaggcgc gtcagtggca tttagcgggt
     1861 ttcggggcgc agccctgaac cagtcacgta gcgctagcgg agtgtatact ggcttactat
     1921 ggtggcacga cgggaatcgg gatgaaatag tcagtcatga aaactgtgag atgaggctca
     1981 ggtgcgtaag aggctgatgc ctgtcccggt ggatattccg cttcctcgct cactgactcg
     2041 ctacgctcgg tcgttcggct gcggcgagcg gtacggactc acggataaag acgtggcggg
     2101 gaaatacgtg aatgcaggag gggaagaaag gatgcgccgc tgccggtttt ccataggctc
     2161 cgcccccctg acaagcatca cagaatctga cgctcaaatc agtggtggcg aaacccgatg
     2221 cggcttaaag ataccaggcg tttccccctg atggctccct cgtgctcccc cgcattcctg
     2281 cctttcggtt taccggtgtc attccgctgt tatggccgcg gtttctcatt ccacgcctga
     2341 cactcagttc cgcgaaggca gttcgctcca ggattgactg tatgcacgaa ccccccgttc
     2401 agtccgactg ctgcgcctta tccggtaact atcgtcttga gtccaacccg gaaagacacg
     2461 aaaaatcgct actggcagca gccattagta actggaggta tacgagagac aaattaagag
     2521 gtcttgaagt atgggcctga gagaggctac actgaaagaa cagttttggt ttctgcggtc
     2581 tcgtataccc agttacctgg ttaagcagtt ccccaactga cttaaccttc gatcaaacca
     2641 cctccccagg tggttttttc gttttcagag caagagatta cgactgtaac gacaggatca
     2701 caagaagatc atttactcag agagactaac taccactatg tttgcctatc aacatactta
     2761 ggaaacatta cttgagttaa cgactccacc ttacttttag tatctcgcaa tgaatcttcc
     2821 gaccgccgtt gtgttgaagt tctattgcgc caccggggta taaatcactt tcgtttaact
     2881 caattaaaag ctcgttcttg tgagcatcct ctaaataaag gtaataacac ccaccataaa
     2941 ggttctgcgt atctggcacg gcaacaaaag atttctttcc gaacagtaaa acagcctctt
     3001 tttctccatg ctctgtcagc aataatcgaa attcttgtcc attcaatcct cttttcgcat
     3061 gaaaaaacga cctatactta gatggttagt gaccatatcc actttacctt taagcaggga
     3121 acctattatg gggtttgagg tccaaccgta cgaaaacgta cggtaagagg aaaattatcg
     3181 tctgaaaaat cgattagtag acaagaaagt ccgttaagtg ccaattttcg attaaaaaga
     3241 caccgttttg atggcgtttt ccaatgtaca ttatgtttcg atatatcaga cagttacttc
     3301 actaacgtac gttttcgttc tattggcctt cagaccccat tatgaataaa aaaacgctgt
     3361 tggcggccat gatggtcgcg ttggtgacct ttgccgctgc tggatgttct tcaaaccaag
     3421 aaataaaaac cacagatgat cgcactatcg ttacagacgg caaacccaaa gttgacagtg
     3481 atacgggatt agtatcctac aaagatgccc atacaggccg aaccgaacag atcaaccgtg
     3541 acaaaattac caacatgagt gaactagaca actgatacgg ataaaaggag ctggctttga
     3601 aaaagatttt tgtttcagtg ttcgcagcgg cagttgcgct ttcagcccta accggctgca
     3661 cgcgcacaag ctatgccatc cacaccaacg acgggcgtac aattgtcagc gacggcaagc
     3721 ctacagaatc agactcaggc ctgctgggct ataaagacgc aaatggtgtc aaacagcaga
     3781 tcaataaagc cgacgttaaa gaagtctctg aaattccgca ttgaggcatc gctctctccg
     3841 aaaagggccg ctaatgcggc ccttttcttt atctgcccca acaacaggca aaaaaagccc
     3901 ccgctggggg ccaaatacct gcagtggctg gatagtactg cattcctgat gaaggagacg
     3961 aataagtatg ggccggattt ttgcgtctgc aggctcggtc gccacaattt ttccgtaccc
     4021 gccaggcatc atgcttttac cataacatcc cttgcccgca cctctccgga cgggttcagc
     4081 gcgaatgcgg cgtcagtcct gcaaaaccga cagtaaacca ccccgcaaac cgtgcattct
     4141 gcgcctgata aatctcaccc gactgcatag ccatgcagcc gggtgaatgg caccgggttt
     4201 cggcgcagat cctcaatgaa agccccgttt tatccggtta tcacagcgac ggaccgtcat
     4261 actcctgctg acgctgcgat cgttccagct ccagcgcttt ctggtgctgc
//
