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Klebsiella pneumoniae strain CRK0078 CRK0078_NODE_70.ctg_1, whole genome shotgun sequence

NCBI Reference Sequence: NZ_NFAW02000036.1

FASTA Graphics 

LOCUS       NZ_NFAW02000036         6656 bp    DNA     linear   CON 19-DEC-2024
DEFINITION  Klebsiella pneumoniae strain CRK0078 CRK0078_NODE_70.ctg_1, whole
            genome shotgun sequence.
ACCESSION   NZ_NFAW02000036 NZ_NFAW02000000
VERSION     NZ_NFAW02000036.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN06812596
            Assembly: GCF_002186215.2
KEYWORDS    WGS; RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Enterobacterales; Enterobacteriaceae; Klebsiella/Raoultella group;
            Klebsiella.
REFERENCE   1  (bases 1 to 6656)
  AUTHORS   Vanduin,D., Fouts,D., Wright,M., Sutton,G., Nguyen,K.,
            Kreiswirth,B., Chen,L., Rojas,L., Hujer,A., Hujer,K., Bonomo,R. and
            Adams,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (18-OCT-2018) Informatics Core Services, JCVI, 9605
            Medical Center Drive, Rockville, MD 20850, USA
REFERENCE   2  (bases 1 to 6656)
  AUTHORS   Fouts,D., Wright,M., Sutton,G., Nguyen,K., Kreiswirth,B., Chen,L.,
            vanDuin,D., Rojas,L., Hujer,A., Hujer,K., Bonomo,R. and Adams,M.
  TITLE     Direct Submission
  JOURNAL   Submitted (02-MAY-2017) JCVI, 9704 Medical Center Drive, Rockville,
            MD 20850, USA
COMMENT     REFSEQ INFORMATION: The reference sequence is identical to
            NFAW02000036.1.
            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 Method        :: SPAdes v. 3.10.0
            Genome Representation  :: Full
            Expected Final Version :: Yes
            Genome Coverage        :: 116.85x
            Sequencing Technology  :: Illumina NextSeq 500
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_002186215.2-RS_2024_12_19
            Annotation Date                   :: 12/19/2024 01:29:06
            Annotation Pipeline               :: NCBI Prokaryotic Genome
                                                 Annotation Pipeline (PGAP)
            Annotation Method                 :: Best-placed reference protein
                                                 set; GeneMarkS-2+
            Annotation Software revision      :: 6.9
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 5,558
            CDSs (total)                      :: 5,479
            Genes (coding)                    :: 5,325
            CDSs (with protein)               :: 5,325
            Genes (RNA)                       :: 79
            rRNAs                             :: 2, 2, 1 (5S, 16S, 23S)
            complete rRNAs                    :: 2, 1, 1 (5S, 16S, 23S)
            partial rRNAs                     :: 1 (16S)
            tRNAs                             :: 62
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 154
            CDSs (without protein)            :: 154
            Pseudo Genes (ambiguous residues) :: 0 of 154
            Pseudo Genes (frameshifted)       :: 49 of 154
            Pseudo Genes (incomplete)         :: 111 of 154
            Pseudo Genes (internal stop)      :: 13 of 154
            Pseudo Genes (multiple problems)  :: 16 of 154
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..6656
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /submitter_seqid="CRK0078_NODE_70.ctg_1"
                     /strain="CRK0078"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /geo_loc_name="USA: Ohio"
                     /collection_date="2013"
                     /collected_by="David van Duin"
     gene            <1..1755
                     /gene="traG"
                     /locus_tag="B9027_RS07415"
                     /old_locus_tag="B9027_007415"
     CDS             <1..1755
                     /gene="traG"
                     /locus_tag="B9027_RS07415"
                     /old_locus_tag="B9027_007415"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_020326930.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer mating-pair stabilization
                     protein TraG"
                     /protein_id="WP_058876160.1"
                     /translation="WLQTWPLLFAILNSAMAYYAKQNGVPVVLSELSQVQLKNSDIAT
                     TAGYIAVMIPPLSWGIVKSMGAAFSSAYSHFSSSGLGATSQAASGVVDGNYSFANMQM
                     ENVSGYSWGTNSTTSFGQMSRQLANGGMSTQTRDGSMVWDSGGAMSKLPVDINVGRQI
                     ASAQQQMAREADVQAESALHGYNSSVTSAWNVLKQFGTNRGTSSSMTTGADNTESSQD
                     TMAKSKMWNAVVANAKANNISNEQSFQNLMDESTRGTVTGEAHVGARWSSGDQLAGKI
                     GKLATGASVEGGIKGSISGSGSTGSTDTVGQSGRHSSDSRHDISSQAAKDFREASDYL
                     VSHKTNTSGNITDNNASSRVDQFAASLSSAKNSYDQYTTSRTRSHEYSEMASRTESLT
                     GQMSENLTQQFANFVQHRAPQDAEAILTNTSSPEIAAQREMLAREFVKAQVEPRIDSS
                     FEQGRNDIGNGMASVSGTPGDQTVVSDFGKHSGDIESMSRNSGIKENVRNQVDSMVED
                     NTRINNAGKINIKEQGEGIKQQNADFEMLHKKEGNDFNERYNKELNGQVNNPLSNTTE
                     EFRKKAEESARKMDGKLP"
     gene            1768..2316
                     /gene="traS"
                     /locus_tag="B9027_RS07420"
                     /old_locus_tag="B9027_007420"
     CDS             1768..2316
                     /gene="traS"
                     /locus_tag="B9027_RS07420"
                     /old_locus_tag="B9027_007420"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004152623.1"
                     /note="TraS, as the term is used in F-like plasmids, is a
                     plasmid entry exclusion protein. It interacts with the
                     F-like plasmid mating stabilization protein TraG; Derived
                     by automated computational analysis using gene prediction
                     method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer entry exclusion protein TraS"
                     /protein_id="WP_004152623.1"
                     /translation="MITNKQILTEVEQLSRLFKDGEADIPSMWNCFWPGLAAMFWLLL
                     WPIAMFSYKLFFVELPNAAQMGIAASVLVAFVAGLFMMLYIVNFRALYLSIPDTYRKQ
                     SALCQFIVGKAKFYCRVYLLTYVFLIISCTYPVYGAIYSTVLFICFSFCLMQIVNVDL
                     SRYQLTALTSLLETFKTSKSEK"
     gene            2500..3231
                     /gene="traT"
                     /locus_tag="B9027_RS07425"
                     /old_locus_tag="B9027_007425"
     CDS             2500..3231
                     /gene="traT"
                     /locus_tag="B9027_RS07425"
                     /old_locus_tag="B9027_007425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229690.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="conjugal transfer complement resistance protein
                     TraT"
                     /protein_id="WP_004152622.1"
                     /translation="MQFNKLMTVMVVSSALALSGCSAMGTAIKKRNLEVKTQMSETIW
                     LEPSNNKTVYLQIKNTSDKDMSGLQAKIASAVTSKGYQVVSNPDTAGYWIQANVLKAD
                     KMDLRESQGWLSRGYEGAVTGAALGAGITAYNSSSAGATLGVGLAAGLVGMAADAMVE
                     DVNYTMITDVQIAERTKTQVQTDNVAVLRQGTSGAKVQTSTETGNQHKYQTRVVSNAN
                     KVNLKFPEAQPVLEDQLAKSIANIL"
     gene            3423..4112
                     /locus_tag="B9027_RS28470"
     CDS             3423..4112
                     /locus_tag="B9027_RS28470"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229689.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004198206.1"
                     /translation="MTISEPVRSLDTHELMPGDIYPHPAVGESYSLSHCEVCSLFSDH
                     FMYICSALVILLLVFIAGVFFRKLMTSSTGRKRDTVSVIPDTKPEAQSKPEYFHLSIC
                     VEGPASTDDSALSSLASRVVREAENLYIPGVNRRDSADDVFAWSVQTQFPSDRLFGTR
                     IFPSTGWFERPDMIKPPVKCYCVCLQYTAETLPSTLHALVDEAGRQVAKSYIKGGHCP
                     GSEGYSFCITS"
     gene            4241..6553
                     /gene="traD"
                     /locus_tag="B9027_RS07435"
                     /old_locus_tag="B9027_007435"
     CDS             4241..6553
                     /gene="traD"
                     /locus_tag="B9027_RS07435"
                     /old_locus_tag="B9027_007435"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004152630.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="type IV conjugative transfer system coupling
                     protein TraD"
                     /protein_id="WP_004152620.1"
                     /translation="MSFNAKDMTQGGQIANMRFRMFGQIANIIFYVLFILFWVLCGLM
                     LMYRLSWQTFVNGCVYWWCTTLGPMRDIIRSQPVYTIQYYGQSLEYTSEQILADKYTI
                     WCGEQLWTGFAFAAVVSLVICIVTFFIASWVLGRQGKQQSEDENTGGRQLSDKPKEVA
                     RQMKRDGVASDIKIGDLPILKNSEIQNFCLHGTVGSGKSEVIRRLLNYVRARGDMAII
                     YDRSCEFVKSYYDPSLDKILNPLDSRCAAWDLWKECLTLPDFDNISNTLIPMGTKEDP
                     FWQGSGRTIFAEGAYLMREDDDRSYEKLVDTMLSIKIDKLRAYLQNTPAANLVEEKIE
                     KTAISIRAVLTNYVKAIRYLQGIEKNGEPFTIRDWMRGVREDRPNGWLFISSNADTHA
                     SLKPVISMWLSIAIRGLLAMGENRNRRVWIFADELPTLHKLPDLVEILPEARKFGGCY
                     VFGIQSYAQLEDIYGVKPAATLFDVMNTRAFFRSPSKEIAEFAAGEIGEKEILKASEQ
                     YSYGADPVRDGVSTGKEKERETLVSYSDIQTLPDLSCYVTLPGPYPAVKLALKYKPRP
                     KIAEGFIPRTLDARVDARLSALLEAREAEGSLARALFTPDTPEPGPADTDSHASEQPE
                     PVSPPAPAVMTVTPAPVKSPPTTKRPAAEPSVRATEPPVLRGTTVPLIKPKAAAAATA
                     ASTASSAGAPAAAAGGTEQELAQQSAEQGQDMLPAGMNEDGVIEDMQAYDAWLADEQT
                     QRDMQRREEVNINHSHRHDEQDDVEIGGNF"
     gene            6553..>6656
                     /locus_tag="B9027_RS29425"
     CDS             6553..>6656
                     /locus_tag="B9027_RS29425"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005229687.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004208632.1"
                     /translation="MMSIGSVKSAGSAGNYYTDKDNYYVIGSMDERWQG"
CONTIG      join(NFAW02000036.1:1..6656)
//
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