LOCUS NZ_AGKA01000245 7017 bp DNA linear CON 19-APR-2025
DEFINITION Yersinia pestis biovar Orientalis str. AS200901509 contig00301,
whole genome shotgun sequence.
ACCESSION NZ_AGKA01000245 NZ_AGKA01000000
VERSION NZ_AGKA01000245.1
DBLINK BioProject: PRJNA224116
BioSample: SAMN01831181
Assembly: GCF_000255895.1
KEYWORDS WGS; RefSeq.
SOURCE Yersinia pestis biovar Orientalis str. AS200901509
ORGANISM Yersinia pestis biovar Orientalis str. AS200901509
Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria;
Enterobacterales; Yersiniaceae; Yersinia.
REFERENCE 1 (bases 1 to 7017)
AUTHORS Gibbons,H.S., Krepps,M.D., Ouellette,G., Karavis,M., Onischuk,L.,
Leonard,P., Broomall,S., Sickler,T., Betters,J.L., McGregor,P.,
Donarum,G., Liem,A., Fochler,E., McNew,L., Rosenzweig,C.N. and
Skowronski,E.
TITLE Comparative genomics of 2009 seasonal plague (Yersinia pestis) in
New Mexico
JOURNAL PLoS One 7 (2), e31604 (2012)
PUBMED 22359605
REFERENCE 2 (bases 1 to 7017)
AUTHORS Gibbons,H.S., Krepps,M., Ouellette,G., Karavis,M., Onischuk,L.,
Leonard,P., Broomall,S., Sickler,T., Betters,J.L., McGregor,P.,
Donarum,G., Liem,A., Fochler,E., McNew,L.A., Rosenzweig,C.N. and
Skowronski,E.
CONSRTM Transformational Medical Technologies Program
TITLE Direct Submission
JOURNAL Submitted (22-SEP-2011) Genomics Integrated Product Team, US Army
Edgewood Chemical Biological Center, 5183 Blackhawk Rd, Aberdeen
Proving Ground, MD 21010-5424, USA
COMMENT REFSEQ INFORMATION: The reference sequence is identical to
AGKA01000245.1.
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-Annotation-Data-START##
Annotation Provider :: NCBI RefSeq
Annotation Name :: GCF_000255895.1-RS_2025_04_15
Annotation Date :: 04/15/2025 13:58:48
Annotation Pipeline :: NCBI Prokaryotic Genome
Annotation Pipeline (PGAP)
Annotation Method :: Best-placed reference protein
set; GeneMarkS-2+
Annotation Software revision :: 6.10
Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA
Genes (total) :: 4,226
CDSs (total) :: 4,155
Genes (coding) :: 3,913
CDSs (with protein) :: 3,913
Genes (RNA) :: 71
rRNAs :: 3, 1, 2 (5S, 16S, 23S)
complete rRNAs :: 3, 1, 1 (5S, 16S, 23S)
partial rRNAs :: 1 (23S)
tRNAs :: 57
ncRNAs :: 8
Pseudo Genes (total) :: 242
CDSs (without protein) :: 242
Pseudo Genes (ambiguous residues) :: 0 of 242
Pseudo Genes (frameshifted) :: 139 of 242
Pseudo Genes (incomplete) :: 114 of 242
Pseudo Genes (internal stop) :: 22 of 242
Pseudo Genes (multiple problems) :: 29 of 242
CRISPR Arrays :: 2
##Genome-Annotation-Data-END##
FEATURES Location/Qualifiers
source 1..7017
/organism="Yersinia pestis biovar Orientalis str.
AS200901509"
/mol_type="genomic DNA"
/submitter_seqid="contig00301"
/strain="AS200901509"
/isolation_source="liver; spleen"
/host="Cynomys gunnisoni"
/sub_species="pestis"
/db_xref="taxon:1084234"
/geo_loc_name="USA: Santa Fe, NM"
/collection_date="07-Jul-2009"
/biovar="Orientalis"
gene complement(53..1180)
/gene="pdxB"
/locus_tag="KOE_RS0119480"
CDS complement(53..1180)
/gene="pdxB"
/locus_tag="KOE_RS0119480"
/EC_number="1.1.1.290"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_005276711.1"
/GO_function="GO:0033711 - 4-phosphoerythronate
dehydrogenase activity [Evidence IEA]"
/GO_function="GO:0046983 - protein dimerization activity
[Evidence IEA]"
/GO_function="GO:0051287 - NAD binding [Evidence IEA]"
/GO_process="GO:0008615 - pyridoxine biosynthetic process
[Evidence IEA]"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="4-phosphoerythronate dehydrogenase PdxB"
/protein_id="WP_002209725.1"
/translation="MKILVDENMPYAEELFRRLGDVQAVPGRPIPRDALVDADALMVR
SVTKVNEALLHGTSIGFVGTATAGTDHVDDTWLRQQGIGFSAAPGCNAIAVVEYVFSA
LMMMAERDGFQLRDKTVGIIGVGNVGSRLNARLQALGVRTLLCDPPRADRGDNEAFWP
LEKLVREADVLTFHTPLNKTGAYQSLHMADDELLAALPDGRILINACRGAVVDNAALL
RALEKGKKLSVVLDVWEPEPDLSLPLLARVDIGTPHIAGYTLEGKARGTTQVFEAFSQ
HLGQPQSVELASLLPVPEFSHLRLNGELDEGKLKRLMHLVYDVRRDDAPLRHVAGLPG
EFDRLRKHYQERREWSSLCVQCDDATSAGLLQQLGFTTQLL"
gene complement(1227..2012)
/locus_tag="KOE_RS0119485"
CDS complement(1227..2012)
/locus_tag="KOE_RS0119485"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_002209724.1"
/GO_function="GO:0003700 - DNA-binding transcription
factor activity [Evidence IEA]"
/GO_function="GO:0043565 - sequence-specific DNA binding
[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="AraC family transcriptional regulator"
/protein_id="WP_002209724.1"
/translation="MTGPDFPVVTSRIPQTLSFRCEAFNANTEFLPHTHPFGQLICVK
SGVLAMSIGGQRFLAPPEFIVWIPAGMEHSSYNRKPMHFRAIDIALDFCTELPASPGL
MNVSPIFNAIVEDCFTRDLLMPETQQDRRLAHVLIDQLKVSPVQRTYLPTSQDKLLSP
ILAALERCPADSTSLALWAKRVYTTERTLSRRCQQELGMAFSEWRQRLRFLHAISLLE
QGKTVNSVALDVGYSSASAFIAMFQQISGTTPERFRRGNSGLY"
gene 2238..3155
/locus_tag="KOE_RS0119495"
CDS 2238..3155
/locus_tag="KOE_RS0119495"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_012303922.1"
/GO_component="GO:0016020 - membrane [Evidence IEA]"
/GO_function="GO:0022857 - transmembrane transporter
activity [Evidence IEA]"
/GO_process="GO:0055085 - transmembrane transport
[Evidence IEA]"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="DMT family transporter"
/protein_id="WP_002209722.1"
/translation="MNVLFPLFAVIIWSVNAVVSKISATAIDPAAISFYRWLLALLTL
SPFLLLGVVRNWQAIRVYWWKLMLLGMLGMVLYQSLAYYAAHSVSALFMGILSSLIPL
LTVLISIVLLRVAPTVGIALGSLLSLGGLVWLISAGNPVQLLQHGIGKGELMMLGASA
SYALYGVLTKRWAIQLPNWQSLYMQIVFGVVLLLPGFLMTPDVQLTAQNIPLVLFAGI
PASILAPYLWIQGVMRLGANTASIFMNLTPVFTAIIAVVFLHEQLHSYHLIGGGITLA
GVVLAQRLRSPLRRNLDLAGHIPNNKNSR"
gene 3440..4477
/gene="flk"
/locus_tag="KOE_RS0119500"
CDS 3440..4477
/gene="flk"
/locus_tag="KOE_RS0119500"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_005171873.1"
/GO_component="GO:0016020 - membrane [Evidence IEA]"
/GO_process="GO:0010468 - regulation of gene expression
[Evidence IEA]"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="flagella biosynthesis regulator Flk"
/protein_id="WP_002209721.1"
/translation="MQPLNGPGVPIGNDRHITPTKLTAQSTVEDQALTPAQRTTLEKL
IVRIMALSPVKSAEIWAGLRHNLSLDATGDLLARHFQPAEQLLQTRLSQAQENHASQQ
LRQQLTALLPQGNNRQAVSDFIRQQFGHTVLSQLSHTELQQVLVLLQSGTLNIPQPQL
TTLTDRPLLPAEHQNIQSLVAKLSAATGEQPTKIWQTLFDMVGVKHHDPLPARHFQLL
SQFLQTKVALSQQTAPTLVNLQTALKQPADAQEQQLLADYSQNRFQASPTTPLTQAQL
NDIINILFAARLEKANAAQYLDEEHKPLQPLINPFIASLPESLQPLLQKPSLVVVALI
IVIAFLLAIFL"
gene complement(4819..5349)
/locus_tag="KOE_RS0119505"
CDS complement(4819..5349)
/locus_tag="KOE_RS0119505"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_011193076.1"
/GO_component="GO:0009289 - pilus [Evidence IEA]"
/GO_process="GO:0007155 - cell adhesion [Evidence IEA]"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="fimbrial protein"
/protein_id="WP_002209720.1"
/translation="MSNFKKSVLVAAVLSLSAFAANAADQGKGKVTFTGSIIEAPCSI
TSEAADQVVELGQISTTSLANMGSSEPRSFSIGLEKCDVATMKNVSVTFDGTPDGVDA
EMLKLIGLADGAGIVITDEAGATIKRGVASVGKTLDQGSNSLKFSAYLKGTSADEGSV
VPGEFSSVANFTLAYN"
gene 6140..6832
/locus_tag="KOE_RS0119510"
CDS 6140..6832
/locus_tag="KOE_RS0119510"
/EC_number="5.1.-.-"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_002209718.1"
/GO_function="GO:0047661 - amino-acid racemase activity
[Evidence IEA]"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="aspartate/glutamate racemase family protein"
/protein_id="WP_002209718.1"
/translation="MKILGLIGGMSWESTIPYYRMINQHVKAQLGGLHSAKIILYSVD
FHEIEQLQAKGDWQTAAQLLSNAAISLKHAGAEVIVVCTNTMHKVADDIEAACGLPLL
HIADATAVQIKQQGIDKIGLLGTRYTMEQGFYRGRLTEKHGIEVITPDDTDREAVNRI
IYEELCLGIISETSRDAYRRVIKKLEAQGVQGIIFGCTEITLLVNAQDASVPVFDTTA
IHASAAADYALQ"
CONTIG join(AGKA01000245.1:1..7017)
//
