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Klebsiella pneumoniae strain KPC94 contig-1000009, whole genome shotgun sequence

NCBI Reference Sequence: NZ_NOVX01000016.1

FASTA Graphics 

LOCUS       NZ_NOVX01000016        10622 bp    DNA     linear   CON 23-NOV-2023
DEFINITION  Klebsiella pneumoniae strain KPC94 contig-1000009, whole genome
            shotgun sequence.
ACCESSION   NZ_NOVX01000016 NZ_NOVX01000000
VERSION     NZ_NOVX01000016.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN06766288
            Assembly: GCF_020615575.1
KEYWORDS    WGS; RefSeq.
SOURCE      Klebsiella pneumoniae
  ORGANISM  Klebsiella pneumoniae
            Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
            Enterobacterales; Enterobacteriaceae; Klebsiella/Raoultella group;
            Klebsiella.
REFERENCE   1  (bases 1 to 10622)
  AUTHORS   Camargo,D.R.A., Alves,C.F.M., Coimbra,R.S., Nicolas,M.F. and
            Vasconcelos,A.T.R.
  TITLE     Direct Submission
  JOURNAL   Submitted (24-JUL-2017) Labinfo, LNCC - Laboratorio Nacional de
            Computacao Cientifica, Rua Getulio Vargas 333, Petropolis, RJ
            25651070, Brazil
COMMENT     REFSEQ INFORMATION: The reference sequence is identical to
            NOVX01000016.1.
            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        :: Newbler v. 3.0
            Expected Final Version :: no
            Genome Coverage        :: 118.0x
            Sequencing Technology  :: Illumina HiSeq
            ##Genome-Assembly-Data-END##
            
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Date                   :: 11/23/2023 03:24:27
            Annotation Pipeline               :: NCBI Prokaryotic Genome
                                                 Annotation Pipeline (PGAP)
            Annotation Method                 :: Best-placed reference protein
                                                 set; GeneMarkS-2+
            Annotation Software revision      :: 6.6
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 6,298
            CDSs (total)                      :: 6,153
            Genes (coding)                    :: 5,949
            CDSs (with protein)               :: 5,949
            Genes (RNA)                       :: 145
            rRNAs                             :: 10, 9, 8 (5S, 16S, 23S)
            complete rRNAs                    :: 9, 1, 1 (5S, 16S, 23S)
            partial rRNAs                     :: 1, 8, 7 (5S, 16S, 23S)
            tRNAs                             :: 106
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 204
            CDSs (without protein)            :: 204
            Pseudo Genes (ambiguous residues) :: 0 of 204
            Pseudo Genes (frameshifted)       :: 75 of 204
            Pseudo Genes (incomplete)         :: 143 of 204
            Pseudo Genes (internal stop)      :: 18 of 204
            Pseudo Genes (multiple problems)  :: 30 of 204
            CRISPR Arrays                     :: 1
            ##Genome-Annotation-Data-END##
FEATURES             Location/Qualifiers
     source          1..10622
                     /organism="Klebsiella pneumoniae"
                     /mol_type="genomic DNA"
                     /submitter_seqid="contig-1000009"
                     /strain="KPC94"
                     /isolation_source="blood isolated from a 12-year-old boy"
                     /host="Homo sapiens"
                     /db_xref="taxon:573"
                     /geo_loc_name="Brazil: City of Juiz de Fora, State of
                     Minas Gerais"
                     /lat_lon="21.764167 S 43.350278 W"
                     /collection_date="2011"
     gene            complement(<1..364)
                     /locus_tag="KPC94_RS05675"
                     /pseudo
     CDS             complement(<1..364)
                     /locus_tag="KPC94_RS05675"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:YP_005226014.1"
                     /note="incomplete; too short partial abutting assembly
                     gap; missing C-terminus; Derived by automated
                     computational analysis using gene prediction method:
                     Protein Homology."
                     /pseudo
                     /codon_start=1
                     /transl_table=11
                     /product="group II intron reverse transcriptase/maturase"
     gene            801..1115
                     /locus_tag="KPC94_RS05680"
                     /old_locus_tag="KPC94_06057"
     CDS             801..1115
                     /locus_tag="KPC94_RS05680"
                     /old_locus_tag="KPC94_06057"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004883458.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004196316.1"
                     /translation="MNVHKSYQTITHYHFDWLTPAGDYPKSAIMVVECKDGRWMIVQE
                     FGEDYGCFEGVLKNECDLITKPTFYPDLRSAAMSGFGMMKQLYPLYDDNLFNEFLSEI
                     PE"
     gene            1124..1633
                     /locus_tag="KPC94_RS05685"
                     /old_locus_tag="KPC94_01084"
     CDS             1124..1633
                     /locus_tag="KPC94_RS05685"
                     /old_locus_tag="KPC94_01084"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004196342.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004196342.1"
                     /translation="MANILMPDCLVKLNNLLQAIENAPVECDGHTLMISSALNHAGIS
                     HQRMCGVVKNPKTYFELYPHFWIEIGEFTLDYRLRIWVELYSGGKLSEGAAHGIFDAR
                     GLEYLYTSGSICPPPALDFNLLNLISDGYYEKINFTELTTLAHSVDISLISDVKNVTN
                     TGVAEYNDN"
     gene            1623..2063
                     /locus_tag="KPC94_RS05690"
     CDS             1623..2063
                     /locus_tag="KPC94_RS05690"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011251275.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004196329.1"
                     /translation="MIINQKILEADITNIINTFERLMDESNKSIIPVKSRHVDGLALF
                     ENMYIRARSKHASLLGKPVLVVSSVSVFITNQGCFSTLLSHLKAHCKNKSYLLKIESV
                     ISQELRRYLASQMFVFIGEEWECGSGYWVPEDDPVYPSLNTLPY"
     gene            2093..2749
                     /locus_tag="KPC94_RS05695"
                     /old_locus_tag="KPC94_06053"
     CDS             2093..2749
                     /locus_tag="KPC94_RS05695"
                     /old_locus_tag="KPC94_06053"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004181937.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004181937.1"
                     /translation="MSTIHLITTCAKKKAGPVHDTVFPYHTTDTEIAYQQWKSLVQSR
                     FTTCNDDIKETENIYCSAHWSTAKSIANSNSHICLWVISAGLGLRHSSDPAIPYDATF
                     TKIGRKSASIWGMLTSDPILPGKVPSLAELFSMYRHDIFIIAASPVYLNAVEDDLVKG
                     VAYLPCPIKQLKIASSAAYNGRLREYVRCGGTRMMKDLNANMTTLNIKHAGMLIHELE
                     "
     gene            complement(3023..3625)
                     /locus_tag="KPC94_RS05700"
     CDS             complement(3023..3625)
                     /locus_tag="KPC94_RS05700"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004181934.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="HAD domain-containing protein"
                     /protein_id="WP_004181934.1"
                     /translation="MAGALFSLSAGGVMFATAVVIIIFSAMLYDSIVKRRSKNINPPE
                     FTGSPQLASCNCSGGTVLLYLDFDGVLHRRMNETFERMPLLEKILKQCPELHIVVSSS
                     WRETMTLEGLKYLFPVAFRHRIIGVTPSLQEVKDTEYVRYRECLLHARHMGVNKFIII
                     DDESHRFPPGCENLVSTNYSEGMTDQTVASVIMKYCQYLT"
     gene            complement(3628..4143)
                     /locus_tag="KPC94_RS05705"
                     /old_locus_tag="KPC94_01086"
     CDS             complement(3628..4143)
                     /locus_tag="KPC94_RS05705"
                     /old_locus_tag="KPC94_01086"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004196349.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004196349.1"
                     /translation="MFEHNIAFNGMMIVIVILSYLLFKSLKSKKRLQHKYDEVFKAFH
                     IANSEYTGGLKEVYKNLSLSNAQLQFLAVYLNQDTVQFDGRNIVCEKEDDVQYILSLI
                     SDSHFWLDKSMKGINEVVNNTDVIKDIKLSLSPFASLGELNVIDDEFKLKNKEFDGFA
                     KLKVKYDVKRG"
     gene            complement(4261..5217)
                     /locus_tag="KPC94_RS05710"
                     /old_locus_tag="KPC94_01087"
     CDS             complement(4261..5217)
                     /locus_tag="KPC94_RS05710"
                     /old_locus_tag="KPC94_01087"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004181932.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_025368585.1"
                     /translation="MNTNVHHVQENFYISLQDCINKEEKTKKTCIEYWRREAERAKEE
                     SARRRALSIKIITEKSMILETLFLNIQKTNALKEQYERNLIAKWGGVIDDDKTKDYGI
                     FLPSLEHLSAYVSCAKNDEYSREVLYNRPELSRGIKYDNSYYCPQEKKFIYMRNDKFR
                     PDLELLTNPPYPDFCKNLLYFYVRSFSLHLKKGEPGKPLEIGIRNSVSKNTYEDLCIG
                     LEILMPYMCKTESGKVIINDEGYLSCDSYYRSILVNPKTGGAELVIYRKGRFDHRQKP
                     NTREPRKWLNEDIIIKEFPNIRIVFLYIISCRYQQHFKNRDI"
     gene            complement(5447..6403)
                     /locus_tag="KPC94_RS05715"
                     /old_locus_tag="KPC94_01088"
     CDS             complement(5447..6403)
                     /locus_tag="KPC94_RS05715"
                     /old_locus_tag="KPC94_01088"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_014386559.1"
                     /GO_function="GO:0016491 - oxidoreductase activity
                     [Evidence IEA]; GO:0015035 - protein-disulfide reductase
                     activity [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DsbA family protein"
                     /protein_id="WP_004196319.1"
                     /translation="MENKQSTKKQTLIHIALVVGGFVAGSVIWGNGSNIMNSNDSANE
                     SVKKQQIELANRFNALAQTANQVNKPAGLVLTEQDKELIGKTAAQYLIEHPENLVEAG
                     KRLEANRDGEKTSDVVNTKDVLLETKFTPNYGPDNADVAVIEFFDYMCHFCQQSSPVL
                     EKAIAENKNVRTFFKDFTIFADRTPISGMGAKIGLYIFNKYGQEKYYEFHNKLMSEAG
                     RAMKDRKDYTPSNLAALVNGLGYKEILDQQGNFLLTVEMRDQLQNVLDANMMLADKLN
                     YSGTPVFIVMNMKNPQNKTTTIMPGAPDFYRLQQAIDKAKGN"
     gene            complement(6463..6804)
                     /locus_tag="KPC94_RS05720"
                     /old_locus_tag="KPC94_01089"
     CDS             complement(6463..6804)
                     /locus_tag="KPC94_RS05720"
                     /old_locus_tag="KPC94_01089"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004883444.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004181929.1"
                     /translation="MGLIRTVVYVGIIGGIFAYTQTKDSLENISVPDAEFPSSISRNN
                     FIQSTWVNEHYTSLKNGPIADGISSILDDAQDIRGSVNNVVMTAGNVDIQKAIQDAVD
                     ELDSNSRKSSK"
     gene            complement(6818..7129)
                     /locus_tag="KPC94_RS05725"
                     /old_locus_tag="KPC94_01090"
     CDS             complement(6818..7129)
                     /locus_tag="KPC94_RS05725"
                     /old_locus_tag="KPC94_01090"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_011251282.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="hypothetical protein"
                     /protein_id="WP_004181928.1"
                     /translation="MKKLIAVAAVVVVSFAAQSSVCGPVACKVTFVDVDGSQKPIMLL
                     DDKVSTRKSSMNRVFDDVYSHGRKVQTDLKSTTPAAGHPDKSSPVQMSRELSPVVIYS
                     A"
     gene            complement(7146..7874)
                     /locus_tag="KPC94_RS05730"
                     /old_locus_tag="KPC94_01091"
     CDS             complement(7146..7874)
                     /locus_tag="KPC94_RS05730"
                     /old_locus_tag="KPC94_01091"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_017900915.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="thioredoxin fold domain-containing protein"
                     /protein_id="WP_004181926.1"
                     /translation="MIKPIAVALILLTPSAYADVDLPAELKDKIEAVGINPVSAEKSP
                     VSGIYSVFSKEGTSYVTSDGEYIFTGNLFKVKGTEVENTTDEFISKGMRSYIEKLDTI
                     TYKAPDEKYVIGVFTDITCGFCQKLHSDLQSYLDKGITIKFIAYPRAGMNSMIARNMA
                     SVWCADDKPAALTRAMKGDGLPEKQPTKACMDSIQSQFNAGNMFKLSGTPSGLSLKGE
                     PMVFAGLRDPDQMLNSLKTANQKK"
     gene            8008..8622
                     /locus_tag="KPC94_RS05735"
                     /old_locus_tag="KPC94_01092"
     CDS             8008..8622
                     /locus_tag="KPC94_RS05735"
                     /old_locus_tag="KPC94_01092"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_004026303.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="lytic transglycosylase domain-containing
                     protein"
                     /protein_id="WP_004026303.1"
                     /translation="MTRLFFGAVLFATLTVNANAAFNPPPDRPKPQNVPETVKNECLT
                     DAARFFGIDRDLVFTLFDNEGGKIGSFVLNTNGTWDIGPMQINSSNLAEVKSHFPAIT
                     WRELAYDACASFWVGTWWLHRKIIDRKGNVFEGIADYNSKTPRVRANYIFKFMERYNR
                     RLQRNGKMMQLNAWTGLDRVKQNPPEVTGKLANNSHQQSWQSYR"
     gene            complement(8890..10173)
                     /locus_tag="KPC94_RS05740"
                     /old_locus_tag="KPC94_01093"
     CDS             complement(8890..10173)
                     /locus_tag="KPC94_RS05740"
                     /old_locus_tag="KPC94_01093"
                     /EC_number="3.6.4.-"
                     /inference="COORDINATES: protein motif:HMM:NF024487.3"
                     /GO_function="GO:0005524 - ATP binding [Evidence IEA];
                     GO:0016887 - ATP hydrolysis activity [Evidence IEA];
                     GO:0004386 - helicase activity [Evidence IEA]; GO:0003676
                     - nucleic acid binding [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="DEAD/DEAH box helicase"
                     /protein_id="WP_223819051.1"
                     /translation="MISNGQAVCKEQEQNNTLLKQAISDLGASWPERTATDERRELSA
                     PWLHERWRKAREDVFIAALDVHRAFIENNPVKMAANIGLAMDWLKGRKLTEKQAGLAL
                     DSLSLVVPVISSTFASMPRMFRDTGQEAIGWLLIDEAGQAQPQHAIGAIWRAKRTVLV
                     GDPKQLEPVSGIPSTVEGALGKHYKIPSCWWPGKVSAQILADQTMDVGTYLPDPESEQ
                     IWVGCPLRVHRRCDDPMFSISNHIAYDGLMVHGKKPGLVDFPESGWLDVKGRTCEGNW
                     VVEEGAAVEKLLLALRHQYSLTPDDVFLISPFKDCAKQLNRIAKRLGFRMDRTGTVHK
                     TQGKEATVVILVLGGNIKSQGAKAWAAEKPNLLNVAVSRAKQRIYVIGERALWEKQPY
                     FSTLSRALGRLDVPVSNSNPRAMSYMEEYLTTEWR"
     gene            complement(10234..>10622)
                     /locus_tag="KPC94_RS05745"
     CDS             complement(10234..>10622)
                     /locus_tag="KPC94_RS05745"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_076611553.1"
                     /GO_process="GO:0015074 - DNA integration [Evidence IEA]"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=3
                     /transl_table=11
                     /product="DDE-type integrase/transposase/recombinase"
                     /protein_id="WP_139834557.1"
                     /translation="SRLTMKALEMAWETRGKPVGVMFHSDQGSHYTSRQFRQLLWRYR
                     IRQSMSRRGNCWDNSPMERFFRSLKNEWVPATGYVSFSDAAHAITDYIVGYYSALRPH
                     EYNGGLPPNESENRYWKNSNAVASFC"
CONTIG      join(NOVX01000016.1:1..10622)
//
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