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Enterobacter chengduensis strain IR5473 Scaffold60, whole genome shotgun sequence

NCBI Reference Sequence: NZ_JADKYK010000060.1

FASTA Graphics 

LOCUS       NZ_JADKYK010000060     12456 bp    DNA     linear   CON 13-OCT-2024
DEFINITION  Enterobacter chengduensis strain IR5473 Scaffold60, whole genome
            shotgun sequence.
ACCESSION   NZ_JADKYK010000060 NZ_JADKYK010000000
VERSION     NZ_JADKYK010000060.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN16561281
            Assembly: GCF_017312015.1
KEYWORDS    WGS; RefSeq.
SOURCE      Enterobacter chengduensis
  ORGANISM  Enterobacter chengduensis
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Enterobacterales; Enterobacteriaceae; Enterobacter; Enterobacter
            cloacae complex.
REFERENCE   1  (bases 1 to 12456)
  AUTHORS   Wang,L.
  TITLE     Genomics of OXA-48-producing Enterobacteriaceae from China
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 12456)
  AUTHORS   Wang,L.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-NOV-2020) Department of Clinical Laboratory, Chinese
            PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing
            100853, China
COMMENT     REFSEQ INFORMATION: The reference sequence is identical to
            JADKYK010000060.1.
            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/
            
            ##Genome-Assembly-Data-START##
            Assembly Date          :: 22-JAN-2019
            Assembly Method        :: SOAPdenovo v. 2.21
            Genome Representation  :: Full
            Expected Final Version :: Yes
            Genome Coverage        :: 100x
            Sequencing Technology  :: Illumina HiSeq
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_017312015.1-RS_2024_10_12
            Annotation Date                   :: 10/12/2024 02:51:26
            Annotation Pipeline               :: NCBI Prokaryotic Genome
                                                 Annotation Pipeline (PGAP)
            Annotation Method                 :: Best-placed reference protein
                                                 set; GeneMarkS-2+
            Annotation Software revision      :: 6.8
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,884
            CDSs (total)                      :: 4,782
            Genes (coding)                    :: 4,652
            CDSs (with protein)               :: 4,652
            Genes (RNA)                       :: 102
            rRNAs                             :: 8, 4, 6 (5S, 16S, 23S)
            complete rRNAs                    :: 7, 1, 1 (5S, 16S, 23S)
            partial rRNAs                     :: 1, 3, 5 (5S, 16S, 23S)
            tRNAs                             :: 75
            ncRNAs                            :: 9
            Pseudo Genes (total)              :: 130
            CDSs (without protein)            :: 130
            Pseudo Genes (ambiguous residues) :: 0 of 130
            Pseudo Genes (frameshifted)       :: 39 of 130
            Pseudo Genes (incomplete)         :: 98 of 130
            Pseudo Genes (internal stop)      :: 18 of 130
            Pseudo Genes (multiple problems)  :: 22 of 130
            CRISPR Arrays                     :: 3
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..12456
                     /organism="Enterobacter chengduensis"
                     /mol_type="genomic DNA"
                     /submitter_seqid="Scaffold60"
                     /strain="IR5473"
                     /host="Homo sapiens"
                     /db_xref="taxon:2494701"
                     /geo_loc_name="China: Beijing"
                     /collection_date="2018-01-12"
     gene            <126..446
                     /gene="trbF"
                     /locus_tag="ITR15_RS23430"
                     /old_locus_tag="ITR15_23410"
                     /pseudo
     CDS             <126..446
                     /gene="trbF"
                     /locus_tag="ITR15_RS23430"
                     /old_locus_tag="ITR15_23410"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020818572.1"
                     /note="internal stop; incomplete; partial in the middle of
                     a contig; missing N-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer protein TrbF"
     gene            443..1492
                     /gene="trbG"
                     /locus_tag="ITR15_RS23435"
                     /old_locus_tag="ITR15_23415"
     CDS             443..1492
                     /gene="trbG"
                     /locus_tag="ITR15_RS23435"
                     /old_locus_tag="ITR15_23415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_006022579.1"
                     /GO_process="GO:0009291 - unidirectional conjugation
                     [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="P-type conjugative transfer protein TrbG"
                     /protein_id="WP_011191356.1"
                     /translation="MKPYFRKAGNPASHTHVLPALRRAAFPVVLLAATALAGCATTNP
                     PPEISYDNAAPAVQTVDPPAPVTVVELPRPLPLPGQLQRVEETRRAPEPSNPTARVNQ
                     ANEAARVQPVRDGFINSMQVYPWTQGALYQVYTAVGQITDIALQPGEQLVGAGPVAAG
                     DTVRWIIGDTESGSGATRQIHILVKPTRADLMTNLVINTNMRTYHMELRSTERTYMAS
                     VSWQYPQDQLIALRRQNAEAQAAQPVASGVDLANVNFRYAIEGDRAPWRPLRAFDDGR
                     QVFIEFPRGIGQGEMPPLFVVGPEGNTSELVNYRVRGHHMIVDRLFAAAELRFGSGRE
                     QKRVRIVRTDGRPTS"
     gene            1489..2709
                     /locus_tag="ITR15_RS23440"
                     /old_locus_tag="ITR15_23420"
     CDS             1489..2709
                     /locus_tag="ITR15_RS23440"
                     /old_locus_tag="ITR15_23420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011191355.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="TrbI/VirB10 family protein"
                     /protein_id="WP_011191355.1"
                     /translation="MSENPPRIEEVPDDDAQPLTGEPVGPAPMRLRAEPPRVTRLSRK
                     VLAGLGLVASVGLGGALIYALQTRDAGRPNDELYSTENRSTADGLAGLPRDYSGVPQL
                     GPPLPGDLGRPILSTQDRGQPVPTPGTATPNPGISPEEQRRLQEIETARTSRLFSGSE
                     SRGTPAAAGAAPALAPVPDLASIGLAPPPATPSAQDRQNAFLNAAADRRTVAPDRVAA
                     PVSPNVLQAGAVISAALITGIRSDLPGQITAQVTENIYDSPTGRILLVPQGTRVVGQY
                     DNNVQFGQSRVLLVWTRLVFPNGRSIVLERQPGADAEGFAGLQDGVDYHWWDLAKAAG
                     LSTLLSVGAELAVDNDDQLVQAIRNGGQDTINDAGQQIVRRQLNVAPTITIRPGFPVR
                     VLVTRDLVLEPYGG"
     gene            2712..2948
                     /locus_tag="ITR15_RS23445"
                     /old_locus_tag="ITR15_23425"
     CDS             2712..2948
                     /locus_tag="ITR15_RS23445"
                     /old_locus_tag="ITR15_23425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_018429611.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF2274 domain-containing protein"
                     /protein_id="WP_026227538.1"
                     /translation="MSKLKLGPIADDKPLKVQVELPAALHQDLVDYAHLLGREQGQSA
                     VDPARLIVPMLQRFIATDRGFAKARRTLTPGSAD"
     gene            complement(2945..3841)
                     /locus_tag="ITR15_RS23450"
                     /old_locus_tag="ITR15_23430"
     CDS             complement(2945..3841)
                     /locus_tag="ITR15_RS23450"
                     /old_locus_tag="ITR15_23430"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_018429612.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LysR family transcriptional regulator"
                     /protein_id="WP_011191354.1"
                     /translation="MPDLTLDLRYLKYAVQVAEAGSFRRAAERLSISQSTVSRRVQLF
                     ERQLGFSLFKRTRAGAGLTPEGERFLQQAVVGARYLRNAATEIRSARKLKTGLVRFGM
                     LEAFPACPIINILSAFRNRHPTIEVKLEEGTSEENTLGVKRGLLDAAISLSASKSPQF
                     QVRRLCEPDLFVALSPLHELAARPQLSWEDVCDEVFLVRSDGAGRELAGILRRMVGAG
                     DGAVQLSIQQVSRETLLTMVEQGFGLTITSVIYRPDIALIPLPSARAPTAAIISSSDN
                     DNPTLPLLLKCFDTPSRAGTTD"
     gene            4209..4631
                     /locus_tag="ITR15_RS23455"
                     /old_locus_tag="ITR15_23435"
     CDS             4209..4631
                     /locus_tag="ITR15_RS23455"
                     /old_locus_tag="ITR15_23435"
                     /inference="COORDINATES: protein motif:HMM:NF013231.5"
                     /GO_function="GO:0003700 - DNA-binding transcription
                     factor activity [Evidence IEA]"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MarR family winged helix-turn-helix
                     transcriptional regulator"
                     /protein_id="WP_223296479.1"
                     /translation="MVLLSMEPGLPISVLATSIGLSHAGTVRLIDRLEREQLVERRRQ
                     ITDRRARFIHLTNSGKKITDALLKAREQVISECISPLSPNDLDILGMLSERLLVANGF
                     DKDGSVSLCHLCGYSRIAPSRGKAKPGRSPRWNVASEG"
     gene            4658..5617
                     /locus_tag="ITR15_RS23460"
                     /old_locus_tag="ITR15_23440"
     CDS             4658..5617
                     /locus_tag="ITR15_RS23460"
                     /old_locus_tag="ITR15_23440"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004099025.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YeeE/YedE thiosulfate transporter family
                     protein"
                     /protein_id="WP_004099025.1"
                     /translation="MGSFALELLLCVLAFGFGYAANQGGTCLVVAAHELHRRQPPKMF
                     VGFLAASAAAGLVAVPIVWTGTLGATLAPSTSINFLLLIGAIAFGLGALINDTCLLGS
                     LARLGDGEMRLLALPLGLTIGILAADHGRFGYDSTWPSLISKPSATGLVTLLAFLVVL
                     VLALVFVSTKSVLRTKPGWSFGASMIGLGITGGLLYALSPAWTFADVIQRALPLRMSP
                     AGEVALTAVISSIAGALTASFRQGNLRLQLPTANGILRSVVGGTLMGIGIALIPGGND
                     GLILAAVPTLSPGGIVAYLLMTTTIVFGFAARGKLFRRCLSRP"
     gene            complement(5656..6042)
                     /locus_tag="ITR15_RS23465"
                     /old_locus_tag="ITR15_23445"
     CDS             complement(5656..6042)
                     /locus_tag="ITR15_RS23465"
                     /old_locus_tag="ITR15_23445"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004099026.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DUF6314 family protein"
                     /protein_id="WP_004099026.1"
                     /translation="MDAALDEITMPTEIVAAIGEGALAYRESGILSLADGRVFSACRQ
                     YRYRLSEDSVVVEFADGPHIGTQFLSLSFSRTDTGLEASGVYACGDDTYHATYRILGP
                     AAFEVVIMVQGPAKAYELVSRYSRSG"
     gene            6313..6801
                     /locus_tag="ITR15_RS23470"
                     /old_locus_tag="ITR15_23450"
     CDS             6313..6801
                     /locus_tag="ITR15_RS23470"
                     /old_locus_tag="ITR15_23450"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004099027.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="YkgB family protein"
                     /protein_id="WP_004099027.1"
                     /translation="MSIFDRYEFLVPEHGRRDLGLLRWALVIVFLWFGAMKFTAYEAY
                     GIAPFIEHSPIMNWLGMFGTQGQSYFIGVIELSTGLVLILGAFRPLFSALGALMSAAT
                     YLITLTFFITTPGVAEQTAGGFPAISAAPGQFLLKDAVLLAASLVLLRASVRHRGALV
                     LS"
     gene            7359..7853
                     /locus_tag="ITR15_RS23475"
                     /old_locus_tag="ITR15_23460"
     CDS             7359..7853
                     /locus_tag="ITR15_RS23475"
                     /old_locus_tag="ITR15_23460"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004099028.1"
                     /GO_function="GO:0003700 - DNA-binding transcription
                     factor activity [Evidence IEA]"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MarR family winged helix-turn-helix
                     transcriptional regulator"
                     /protein_id="WP_004099028.1"
                     /translation="MISDDIVRASSSRAPEAGPAASALALLAHKPGLSIRMLAIGVGL
                     SHAGTVRLVDRLVSEGLIERREHSTDGRARSLYLTPTGKVASDEVLASRDQVIAEGLS
                     ILNPDELKTLSDIAERVLRNRLENLEQSYRICRLCCYEGCTNCPVDAELHERGVDREK
                     NDDA"
     gene            complement(8250..9275)
                     /locus_tag="ITR15_RS23480"
                     /old_locus_tag="ITR15_23465"
     CDS             complement(8250..9275)
                     /locus_tag="ITR15_RS23480"
                     /old_locus_tag="ITR15_23465"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004357654.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="zinc-binding alcohol dehydrogenase family
                     protein"
                     /protein_id="WP_004357654.1"
                     /translation="MMTETVTNQAAWQKAPGQPLRIGVTALPHLAANEILIRNAAIAI
                     NPLDWILQDVALLPWLDYPAILGSDVSGEVAAVGGAVERFKVGDRVIGQAVGTTVNQP
                     AQGAFQHHTIVLDHMAAPIPNNIAFADAAVLPLGLGTAASGLYGRTQLALAPPLHSPT
                     ARPEVVLVWGGSSSVGCNAIQLAVASGYRCVATASARNVGLLKELGASEVLDHSSPAI
                     VEDVIEAMRGRSLAGTLHATGHMKDCFAVVARCEGSRRVAATLAPPDERSFGVEATHI
                     SGTSLKDDEVGPMIYREFLPQALAARTFVPAPPAKIVGQGLEMLQAALEALKAGVSAA
                     KIVVTLP"
     gene            complement(9275..9838)
                     /gene="msrA"
                     /locus_tag="ITR15_RS23485"
                     /old_locus_tag="ITR15_23470"
     CDS             complement(9275..9838)
                     /gene="msrA"
                     /locus_tag="ITR15_RS23485"
                     /old_locus_tag="ITR15_23470"
                     /EC_number="1.8.4.11"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_003464967.1"
                     /GO_function="GO:0033744 -
                     L-methionine:thioredoxin-disulfide S-oxidoreductase
                     activity [Evidence IEA]; GO:0008113 - peptide-methionine
                     (S)-S-oxide reductase activity [Evidence IEA]"
                     /GO_process="GO:0030091 - protein repair [Evidence IEA];
                     GO:0006979 - response to oxidative stress [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="peptide-methionine (S)-S-oxide reductase MsrA"
                     /protein_id="WP_011191350.1"
                     /translation="MSQSPTGNRAAATERAILAGGCFWGMEDLLRRARGVISTRVGYT
                     GGEMPDPTYARHYGHAEAVEVTFDPSVLAYRSLLELFFQIHDPTTYEQQGSDVGPSYR
                     SAIFYTTEVQKEVALTTIAEIEASGSWPGPVVSEINPEEPFWEAEPEHQEYLVRYPGG
                     YSCHFVRPTWRLDRSDERPAVILDRKS"
     gene            complement(9871..11103)
                     /locus_tag="ITR15_RS23490"
                     /old_locus_tag="ITR15_23475"
     CDS             complement(9871..11103)
                     /locus_tag="ITR15_RS23490"
                     /old_locus_tag="ITR15_23475"
                     /EC_number="1.11.1.-"
                     /EC_number="3.-.-.-"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_018429618.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="bifunctional alpha/beta hydrolase/OsmC family
                     protein"
                     /protein_id="WP_032640617.1"
                     /translation="MDMAGRSFTFVSGAGSPLSGHLEPPEGTPRGWAIFAHCFTCGKD
                     SRAAVHISRALSRAGIGVLRFDFAGTGIGGGTGEPVNFASDVEDLRAAANAMAAAGMS
                     PSLLVGHSLGGTAAIVAAADMPDIAAVATIGAPADLQHILRLFGPNDLDTIASEGEAS
                     VEIAGRPFLIRRGFLEAVEGIDVEKAIASLRRPVLVMHSPLDQVVGIDHASRIFVASR
                     HPKSFISLDNADHLLTDVADANYAAATVAVWASRFLPPLSADLPQVEVAEGVVSTETL
                     AGTFQLKVRSGEHTLFADEPASVGGLGTGLSPYELVSAGLAACTVMTMRLYANRKGFP
                     LERASTTVQHEKVPDMMPPDRFTRTIVLDGPLSDDQRARILAIADRCPVDLSLIRGSD
                     VQTELLSASQAADPARLA"
     gene            11332..12207
                     /locus_tag="ITR15_RS23495"
                     /old_locus_tag="ITR15_23480"
     CDS             11332..12207
                     /locus_tag="ITR15_RS23495"
                     /old_locus_tag="ITR15_23480"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_018429619.1"
                     /GO_function="GO:0003677 - DNA binding [Evidence IEA];
                     GO:0003700 - DNA-binding transcription factor activity
                     [Evidence IEA]"
                     /GO_process="GO:0006355 - regulation of DNA-templated
                     transcription [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="LysR family transcriptional regulator"
                     /protein_id="WP_011191349.1"
                     /translation="MELNQVSYFINLAETLNFTAAARLSGVSQPSLTRAIRRLEDELG
                     GPLIYRDGKNSRLTGLGHDVEAEFRRMVVAMKSVRNHSEHWAMGGHRVLDVAVAPTVG
                     PKEFTAFFESALAEMPSIEIKLHSLQSNEDTSEVLSGKYHACIMPRETRPERKLDVHP
                     LFRERFVLGCSANHPLAANEIVRGEDLLEFPFVDRLKCEFRDRILDHFARRDLLMRPR
                     FRSDREDWVQRVVADGHAICILPERSPTVQGLVTRPIDGFVLEREVVIATVSGSTATV
                     EIRNIAQLAARYEWN"
     gene            complement(12353..>12456)
                     /locus_tag="ITR15_RS24505"
     CDS             complement(12353..>12456)
                     /locus_tag="ITR15_RS24505"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_001395480.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=3
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_046276267.1"
                     /translation="HQCRSMWQLLKKVRHFMETASPFPGGKHGQAKV"
CONTIG      join(JADKYK010000060.1:1..12456)
//
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