LOCUS NC_005007 4679 bp DNA circular CON 22-FEB-2023
DEFINITION Staphylococcus epidermidis ATCC 12228 plasmid pSE-12228-02,
complete sequence.
ACCESSION NC_005007
VERSION NC_005007.1
DBLINK BioProject: PRJNA224116
BioSample: SAMN02603126
Assembly: GCF_000007645.1
KEYWORDS RefSeq.
SOURCE Staphylococcus epidermidis ATCC 12228
ORGANISM Staphylococcus epidermidis ATCC 12228
Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
Staphylococcus.
REFERENCE 1 (bases 1 to 4679)
AUTHORS Zhang,Y.Q., Ren,S.X., Li,H.L., Wang,Y.X., Fu,G., Yang,J., Qin,Z.Q.,
Miao,Y.G., Wang,W.Y., Chen,R.S., Shen,Y., Chen,Z., Yuan,Z.H.,
Zhao,G.P., Qu,D., Danchin,A. and Wen,Y.M.
TITLE Genome-based analysis of virulence genes in a non-biofilm-forming
Staphylococcus epidermidis strain (ATCC 12228)
JOURNAL Mol Microbiol 49 (6), 1577-1593 (2003)
PUBMED 12950922
REFERENCE 2 (bases 1 to 4679)
AUTHORS Zhang,Y., Ren,S., Li,H., Fu,G., Lu,L., Lu,G., Jia,J., Tu,Y.,
Qin,Z., Chen,Z. and Wen,Y.
TITLE Direct Submission
JOURNAL Submitted (05-NOV-2002) Chinese National Human Genome Center at
Shanghai, 250 Bi Bo Road, Shanghai 201203, China
COMMENT REFSEQ INFORMATION: The reference sequence is identical to
AE015931.1.
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 Date :: 02/22/2023 13:57:34
Annotation Pipeline :: NCBI Prokaryotic Genome
Annotation Pipeline (PGAP)
Annotation Method :: Best-placed reference protein
set; GeneMarkS-2+
Annotation Software revision :: 6.4
Features Annotated :: Gene; CDS; rRNA; tRNA; ncRNA
Genes (total) :: 2,433
CDSs (total) :: 2,352
Genes (coding) :: 2,280
CDSs (with protein) :: 2,280
Genes (RNA) :: 81
rRNAs :: 6, 5, 5 (5S, 16S, 23S)
complete rRNAs :: 6, 5, 5 (5S, 16S, 23S)
tRNAs :: 61
ncRNAs :: 4
Pseudo Genes (total) :: 72
CDSs (without protein) :: 72
Pseudo Genes (ambiguous residues) :: 0 of 72
Pseudo Genes (frameshifted) :: 47 of 72
Pseudo Genes (incomplete) :: 37 of 72
Pseudo Genes (internal stop) :: 22 of 72
Pseudo Genes (multiple problems) :: 25 of 72
##Genome-Annotation-Data-END##
COMPLETENESS: full length.
FEATURES Location/Qualifiers
source 1..4679
/organism="Staphylococcus epidermidis ATCC 12228"
/mol_type="genomic DNA"
/strain="ATCC 12228"
/db_xref="ATCC:12228"
/db_xref="taxon:176280"
/plasmid="pSE-12228-02"
gene join(4400..4679,1..236)
/locus_tag="SE_RS11820"
CDS join(4400..4679,1..236)
/locus_tag="SE_RS11820"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_002502825.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="DUF334 domain-containing protein"
/protein_id="WP_002498954.1"
/translation="MNLSDEDKLYISRMTDQIKRSNTHEIKVNIETDDNLSEFIKQKI
DEKFDEKIPNLRTKQTMEQFKWSLMRIEDKQEILDDNIESVHKWATYFKSALMLTLFA
VLLISVVATFMGGLFNVLGFDHMYKGLEYQIKHSEGFVAFLWHLGYLIPYLLLATLIW
LILALEHKYRY"
gene 598..909
/locus_tag="SE_RS11825"
/old_locus_tag="p201"
/old_locus_tag="SE_p201"
CDS 598..909
/locus_tag="SE_RS11825"
/old_locus_tag="p201"
/old_locus_tag="SE_p201"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_002498949.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="hypothetical protein"
/protein_id="WP_011117534.1"
/translation="MKLKKVIVTVMFLLVIIFSLNIIIRFQYTESKVRSYLVNIEKKP
KKIELKKRIGNLPGYRNYLIEYKEKDTTKYYYYDYKAKQVKGEEQIINGYSKDLKTKS
Q"
gene complement(930..1481)
/locus_tag="SE_RS11830"
/old_locus_tag="p202"
/old_locus_tag="SE_p202"
CDS complement(930..1481)
/locus_tag="SE_RS11830"
/old_locus_tag="p202"
/old_locus_tag="SE_p202"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_002498950.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="YiiX/YebB-like N1pC/P60 family cysteine
hydrolase"
/protein_id="WP_002498950.1"
/translation="MNRNNIFIKILFITSFAMILAIVSNHNQTFALTYKKGDVLTTRS
TSASGLTGHNGIYIGNGKVLDTPRVHHYPRVMSVKKWIKSYPKTKVTRPKNSSLGNKA
ANNAVKYFKGKKIPYKVTPNPKNIKKTYCSEIVWYSYYKAGKQYMIPEHGVWLPPSIV
APYAFVNKQDVKHNGFKFVDNKW"
gene 1769..2689
/locus_tag="SE_RS11835"
/old_locus_tag="p203"
/old_locus_tag="SE_p203"
CDS 1769..2689
/locus_tag="SE_RS11835"
/old_locus_tag="p203"
/old_locus_tag="SE_p203"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_002958488.1"
/GO_function="GO:0003677 - DNA binding [Evidence IEA]"
/GO_function="GO:0003916 - DNA topoisomerase activity
[Evidence IEA]"
/GO_process="GO:0006270 - DNA replication initiation
[Evidence IEA]"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="replication initiation factor domain-containing
protein"
/protein_id="WP_011117535.1"
/translation="MSKKNHSNHLRNKDLDNFSKTGYSNSRLNRHTMYTPEPKLSFDA
MTIVGNLNKNNAHKLSEFMSIEPQIRLWDILQTKFKAKALQEKVYIEYDKVKADTWDR
RNMRVEFNPNKLTHEEMLWLKQNVIDYMEDDGFTRLDLAFDFEDDLSDYYAMTDKSVK
KTIFYGRNGKPETKYFGVRDSDRFIRIYNKKQERRDNANIEVVSEHLWRVEIELKRGM
VDYWNDCFGDLHILQPDWKTIERTSDRSMVFMLLNDEEEWGKLERRTKNKYKQLIKEI
SPVDLTELMKLTLKANEKQLQKQIDFWLIK"
gene 2705..2926
/locus_tag="SE_RS11840"
/old_locus_tag="p204"
/old_locus_tag="SE_p204"
CDS 2705..2926
/locus_tag="SE_RS11840"
/old_locus_tag="p204"
/old_locus_tag="SE_p204"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_002958486.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="hypothetical protein"
/protein_id="WP_011117536.1"
/translation="MSDMFEVDREIKNTYLKMSIGKNTCPKCNSIFEVSVFNDDFPNR
ENELVSCPYCSSLVGYVRTSGTVRSYKIN"
gene 3197..3580
/gene="mobC"
/locus_tag="SE_RS11845"
/old_locus_tag="p205"
/old_locus_tag="SE_p205"
CDS 3197..3580
/gene="mobC"
/locus_tag="SE_RS11845"
/old_locus_tag="p205"
/old_locus_tag="SE_p205"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_002449121.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="plasmid mobilization relaxosome protein MobC"
/protein_id="WP_002498952.1"
/translation="MSEQNTFVASDETVGRNRKPNRKEPKQISFRVSESEYLKLRQSA
ETLNMSVPAFVKKKAQGSRLVAPKFDKETRQSIARDLSKLGANANQIAKYCNKHQHEA
PNYIALEHNINELRERLDEIWQQLN"
gene 3562..4413
/locus_tag="SE_RS11850"
/old_locus_tag="p206"
/old_locus_tag="SE_p206"
CDS 3562..4413
/locus_tag="SE_RS11850"
/old_locus_tag="p206"
/old_locus_tag="SE_p206"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_011117537.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="relaxase/mobilization nuclease domain-containing
protein"
/protein_id="WP_011117537.1"
/translation="MATTKLGNTKSASRAINYAEKRAEEKSGLNCDIDYAKSSFKQTR
ALYGKENGVQAHTVIQSFKPGEVTPEQCNQLGLELAEKIAPNHQVAVYTHADTNHVHN
HIVINSIDLETGKKYQSNKKQREFVKQKNDEVCREHGLSVTERNATMRYTQAEKGLIE
KDKSSWKDEIRDAIEQSQATNFEELERELNQLDITIDRVTNKTITYRHLKENKKVRGK
NLGEQFDKGALENEFAVANERREFEQQLSEYEPRESEYRPRDTEKNIKRPKELRVQSR
ENDFELE"
CONTIG join(AE015931.1:1..4679)
//
