LOCUS       NZ_CP039330             4251 bp    DNA     circular CON 22-APR-2024
DEFINITION  Citrobacter portucalensis strain Effluent_1 plasmid unnamed3,
            complete sequence.
ACCESSION   NZ_CP039330
VERSION     NZ_CP039330.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN11268905
            Assembly: GCF_004801555.1
KEYWORDS    RefSeq.
SOURCE      Citrobacter portucalensis
  ORGANISM  Citrobacter portucalensis
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
REFERENCE   1  (bases 1 to 4251)
  AUTHORS   REHAB consortium,T.
  TITLE     The impact of sequencing depth on the inferred taxonomic composition
            and AMR gene content of metagenomic samples
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 4251)
  AUTHORS   Shaw,L.P.
  TITLE     Direct Submission
  JOURNAL   Submitted (04-APR-2019) Modernising Medical Microbiology Consortium,
            University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU,
            United Kingdom
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. v0.4.0
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 30x
            Sequencing Technology :: Hybrid assembly: Illumina HiSeq 4000 and
            PacBio RSII
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_004801555.1-RS_2024_04_22
            Annotation Date                   :: 04/22/2024 04:13:00
            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)                     :: 5,077
            CDSs (total)                      :: 4,960
            Genes (coding)                    :: 4,846
            CDSs (with protein)               :: 4,846
            Genes (RNA)                       :: 117
            rRNAs                             :: 9, 8, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 8, 8 (5S, 16S, 23S)
            tRNAs                             :: 83
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 114
            CDSs (without protein)            :: 114
            Pseudo Genes (ambiguous residues) :: 0 of 114
            Pseudo Genes (frameshifted)       :: 24 of 114
            Pseudo Genes (incomplete)         :: 80 of 114
            Pseudo Genes (internal stop)      :: 24 of 114
            Pseudo Genes (multiple problems)  :: 13 of 114
            Pseudo Genes (short protein)      :: 1 of 114
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP039330.1.
            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..4251
                     /organism="Citrobacter portucalensis"
                     /mol_type="genomic DNA"
                     /strain="Effluent_1"
                     /isolation_source="Treated sewage effluent"
                     /db_xref="taxon:1639133"
                     /plasmid="unnamed3"
                     /geo_loc_name="United Kingdom: Cholsey Sewage Treatment
                     Works"
                     /lat_lon="51.58 N 1.15 W"
                     /collection_date="2016"
     gene            132..608
                     /locus_tag="E7703_RS25695"
                     /old_locus_tag="E7703_25845"
     CDS             132..608
                     /locus_tag="E7703_RS25695"
                     /old_locus_tag="E7703_25845"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_016246513.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_226564495.1"
                     /translation="MSFTVASAENITHTKPLARSDLYLTCKGYQVKGASVINVEKPSYL
                     EGTGEQVEFAIISLGDASDGLKVFFDSWGFSPFGLIESHVMHEHWSLVHVGGRVSVKGE
                     KIDYSFVDNQPQEGGSYKPKTGVFLYGCINSDKRPSWVEKIYTRTGVFRGGIED"
                     /name="hypothetical protein"
     gene            864..1277
                     /locus_tag="E7703_RS25700"
                     /old_locus_tag="E7703_25850"
     CDS             864..1277
                     /locus_tag="E7703_RS25700"
                     /old_locus_tag="E7703_25850"
                     /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_023206708.1"
                     /translation="MKIIKWASLSGVLLISACGVSQNEVNSANYGSKPIDNDAKVIGMI
                     KESLKDPDSLKVISITTPARGFSKYGFGSTEHGWFTTITYNAKNSYGGYVGAKSSTFVY
                     LNGDYKVAVPMSNGERVMLDKVSFSCKDNCQTK"
                     /name="hypothetical protein"
     gene            complement(1305..1460)
                     /locus_tag="E7703_RS25900"
     CDS             complement(1305..1460)
                     /locus_tag="E7703_RS25900"
                     /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_167493803.1"
                     /translation="MNSKQKCSHSNLEKEYYLGSATGDYKCLDCGEVGFGKDWPEKERS
                     KNDNEA"
                     /name="hypothetical protein"
     gene            2507..2830
                     /locus_tag="E7703_RS25715"
                     /old_locus_tag="E7703_25865"
     CDS             2507..2830
                     /locus_tag="E7703_RS25715"
                     /old_locus_tag="E7703_25865"
                     /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_170874913.1"
                     /translation="MLTMWVTEDEHRRLLDRCDGKQLAAWMRQTCLDEKPARAGKLPSL
                     SPALLRQLAGMGNNLNQIARQVNAGGGSGHDRVQVVAALMAIDAGLERLRHAVLEKGAD
                     DDR"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            3039..>3473
                     /locus_tag="E7703_RS26160"
                     /pseudo=""
     CDS             3039..>3473
                     /locus_tag="E7703_RS26160"
                     /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            3508..3993
                     /locus_tag="E7703_RS25725"
     CDS             3508..3993
                     /locus_tag="E7703_RS25725"
                     /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_023139312.1"
                     /translation="MNSLLTLAKDLEQKSKAQQQSTGEMLKAAFSEHEKSVRAELSESE
                     KRISAAILDHDRKLSSAMSQRTKGMVRMVSQTWLTIVLVSALLTASGASILWWQGQQIL
                     DNYTTIREQKRTQAMLSERNSGVQLSTCGEQRRRCVRVNPEAGRFGEDSSWMILAGK"
                     /name="MbeB family mobilization protein"
     gene            3997..4212
                     /locus_tag="E7703_RS25730"
     CDS             3997..4212
                     /locus_tag="E7703_RS25730"
                     /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_058671277.1"
                     /translation="MTELEKQLLSALEQLQQDYSKRLDEWENAFAEWRTMSGLMQRENA
                     ALSERVTGLSRQVQSLSDQLRRLSKG"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          complement(1752..2241)
                     /name="rep_cluster_2335"
                     /typing="replicon"
                     /tool="MOB-suite"
                     /identity="94.501"
                     /coverage="81.0"
                     /evalue="0.0"
     Typing          2821..4250
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.034"
                     /coverage="96.0"
                     /evalue="0.0"
ORIGIN
        1 agcatcagaa aacgctggag ctggaacgat cgcagcggca gaaaggtttt gagcttggaa
       61 tgtagttaat caatgaaaag ggatgcgtta tgaagtgttt ctgggcttgc tcagtctcag
      121 tagttttggt tatgtcattt acagtcgctt ctgcggagaa cattacacac acaaaaccgt
      181 tagccaggag cgacttatat cttacctgta aaggttatca ggtgaagggg gcgtctgtaa
      241 ttaacgtcga gaaaccttct taccttgaag gtacaggtga gcaggttgag tttgcaatca
      301 tttctctcgg tgatgcatct gatggactca aggttttttt tgattcatgg ggtttttctc
      361 cttttggatt gattgaaagt catgtaatgc atgagcactg gtctttagtt catgttgggg
      421 ggcgtgtttc agtcaagggt gaaaagattg attattcatt tgtagataac cagccacagg
      481 agggtgggag ctataaaccc aaaacaggtg tgttcctgta tggctgcatt aactctgata
      541 aaaggccatc ttgggtcgaa aaaatctaca caagaacagg cgtgtttcga gggggcatag
      601 aagactaaaa tactgcgtac agcatgaaaa ttcattgaac agagtgttag ttcattttcg
      661 tgcatggcta tgcatacacg caaaacttat cagcgcgatt ccgggcggtt ttcggtgaga
      721 agacgggctc ttttgtggct taggacggaa aaacgccctg agcgcgtctg agcggtgcgc
      781 ccaagagatg ttatggtaaa tctatctata aatgtctata tagtggattt cctatagttg
      841 tttggaaaat gacaaggata tatatgaaaa taattaagtg ggcttcactg tctggtgttc
      901 tgttaatatc tgcttgtggt gtttctcaga acgaagtaaa tagtgctaat tatggttcaa
      961 aaccaataga taatgatgcg aaagtgattg gtatgattaa agagagtcta aaagatcctg
     1021 attctctaaa agttatatca ataaccaccc ccgccagagg tttttctaag tatggctttg
     1081 gctctacaga gcatggctgg ttcactacta tcacatataa tgcaaaaaac tcttatggcg
     1141 gttatgttgg tgctaagtcc agtactttcg tttacttaaa cggagattat aaagtggcag
     1201 tgccaatgtc taatggtgag agggttatgt tagataaagt gtcattttca tgtaaagaca
     1261 attgccaaac taaatgataa aaaaggccgc aatagcggcc ttttttatgc ttcgttatca
     1321 tttttacttc tttctttttc tggccagtcc ttcccaaaac caacctcccc gcaatccaaa
     1381 catttataat cgcctgtggc gctacccaag tagtattctt tttctagatt tgaatgagaa
     1441 catttttgtt tgctgttcac tacagtcacc tttggatatt catttattcg tgaatgattt
     1501 ttatctatac cgacattgtt aaatgatgga aagatcttct tgagatcctt tttttctacg
     1561 cgtaatcttc atgactgtaa acgaaaaaac caccctggca ggtggttttt cgaaggttag
     1621 ttaatcctgg cagattctct aaccgtggta acagtcttgt gcgagacatg tcaccaaatc
     1681 tgtccttcca gtgtagcctc agtcaggccg ccacttcaag aactctgaac acatctctcg
     1741 cacaaacctg ttaccagtgg ctgctgccag tggcgttttg tcgtgtcttt ccgggttgga
     1801 ctcaagacga tagttaccgg ataaggcgca gcagtcggac tgaacggggg gttcgtgcat
     1861 acagtccagc ttggagcgaa ctgcctaccc ggaactgagt gtcaggcgtg gaatgagaca
     1921 aacgcggcca taacagcgga atgacaccgg taaaccgaaa ggcaggaaca ggagagcgca
     1981 cgagggagcc accaggggga aacgcctggt atctttaagt cctgtcgggt ttcgccacca
     2041 ctgatttgag cgtccgattc tgtgatgctt gtcagggggg cggagcctat ggaaaaacgg
     2101 cagcgccgcg gccttctcgt ttccctgtta agttccctcc tggcatctcc ccggaaattt
     2161 ccgccccatt cgtaagccgg taccgctcgc cgcagccgaa cgaccgagcg tagcgagtca
     2221 gtgagcgagg aagcggaata tcaccggtcc tgcattttct gcttacgcgc ccgccatggc
     2281 attacacctg ctttatgtgg catctatgca ttatgtttct gcgatgttac attttaagcc
     2341 agtatacact ccgctagcgc tacgtgactg gttcagggct gcgccccgaa acccgctaaa
     2401 accactgacg cgcctgcggc ttgtccaaca ccgcgccgac cgggaaaaga tttccagccc
     2461 gtcccggcgt tatcaggagg ccggattggc agacaaacgc agcaaaatgc tcacgatgtg
     2521 ggtgaccgaa gatgagcacc gccgtctgct ggatcgctgc gacggtaaac agcttgcagc
     2581 ctggatgcgc cagacgtgcc tggacgagaa acccgcccgc gccggcaagc ttccctcgct
     2641 ctcgccggcg ctgcttcgtc agcttgccgg catggggaac aacctcaacc agattgcccg
     2701 gcaggttaac gccggtggtg gcagcgggca cgaccgcgtg caggtcgtcg ccgcgctgat
     2761 ggccatagat gccggactcg agcggctgcg gcatgctgtg ctggaaaagg gtgcagacga
     2821 tgatcgttaa gtttcacccg cgagggcgcg gcggtggcgc cggtccggtg gattatctgc
     2881 tggggaaaga ccgacagcgc gacggcgcca ccgttctgca ggggaagccg gaagaagtca
     2941 gggagcttat cgacgcctcg ccctacgcaa aaaagtacac atccggcgtc ctgtcctttg
     3001 ccgaaaagga tttaccgccc gggcagcgcg aaaagctgat ggcgagcttt gaacgtgttc
     3061 tgatgcccgg actcgataaa gaccagtaca gcgtgctgtg ggttgagcac caggataagg
     3121 ggcggctgga gctgaacttc ctgatcccga acacggagct gctgaccggc aagcgtctcc
     3181 agccgtatta cgaccgcgcc gaccgtccgc gcattgatgc ctggcagacc atcgtgaacg
     3241 gcaggctggg gctgcatgac ccgaacgcgc ctgaaaaccg gcgggcgctg gtcacgccgt
     3301 ccgcgctgcc ggaaacgaag caggaagccg ctcaggcaat tacacggggt ttactggcct
     3361 tagcctcgtc cggggagctg aaaacccgcg aggacgtcac tgaggcgctg gaaagcgcag
     3421 gttttgaggt ggtacgcacc acaaaaagca gcatcagcat tgccgacccg gacggggggc
     3481 gaaacatccg actgaaggga gccatctatg aacagtcttt taacgctggc aaaggactta
     3541 gagcagaaat cgaaagcgca gcagcagagt accggcgaga tgctgaaagc cgcattcagc
     3601 gagcacgaga agtctgtcag agcggaactg agcgaaagcg agaagagaat cagcgccgcc
     3661 atcctcgacc acgaccggaa gctgtcctca gccatgagcc agcgcacgaa aggcatggtg
     3721 cgtatggtca gccagacgtg gctgaccatc gtcctggtgt ctgcactgct gacagcatcg
     3781 ggcgcaagca ttctgtggtg gcaggggcag cagatactcg acaattacac gaccatccgg
     3841 gagcagaagc gcacgcaggc catgctgtcc gagaggaaca gcggcgtgca gctctcgacc
     3901 tgcggagagc agagacgccg ctgcgtgagg gtgaacccgg aagcgggacg gttcggagag
     3961 gattcgagct ggatgatact ggcggggaaa tagcacatga cggagctgga aaaacagttg
     4021 ctgagcgcat tagagcagct acagcaggac tactcgaaaa ggctggacga gtgggagaac
     4081 gccttcgcgg aatggcggac gatgtctggt cttatgcaac gggagaacgc ggcgctgagc
     4141 gagcgcgtca cgggcttgag caggcaggtg cagagtttga gcgatcagct gcgccggttg
     4201 tcgaaaggct gaactcgatt gaagtacaca ggcagcagga gcgggcggcg c
//
