LOCUS NC_012001 4226 bp DNA circular CON 24-DEC-2022
DEFINITION Macrococcus caseolyticus JCSC5402 plasmid pMCCL6, complete
sequence.
ACCESSION NC_012001
VERSION NC_012001.1
DBLINK BioProject: PRJNA224116
BioSample: SAMD00060930
Assembly: GCF_000010585.1
KEYWORDS RefSeq.
SOURCE Macrococcus caseolyticus JCSC5402
ORGANISM Macrococcus caseolyticus JCSC5402
Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
Macrococcus.
REFERENCE 1
AUTHORS Baba,T., Kuwahara-Arai,K., Uchiyama,I., Takeuchi,F., Ito,T. and
Hiramatsu,K.
TITLE Complete genome sequence of Macrococcus caseolyticus strain
JCSCS5402, [corrected] reflecting the ancestral genome of the
human-pathogenic staphylococci
JOURNAL J Bacteriol 191 (4), 1180-1190 (2009)
PUBMED 19074389
REMARK Erratum:[J Bacteriol. 2009 May;191(10):3429]
REFERENCE 2 (bases 1 to 4226)
AUTHORS Baba,T., Kuwahara-Arai,K., Takeuchi,F. and Hiramatsu,K.
TITLE Direct Submission
JOURNAL Submitted (26-JUL-2007) Contact:Tadashi Baba Juntendo University
School of Medicine, Department of Bacteriology; 2-1-1 Hongo,
Bunkyo, Tokyo 113-8421, Japan
COMMENT REFSEQ INFORMATION: The reference sequence is identical to
AP009490.1.
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 :: 12/24/2022 01:10:07
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) :: 2,386
CDSs (total) :: 2,319
Genes (coding) :: 2,275
CDSs (with protein) :: 2,275
Genes (RNA) :: 67
rRNAs :: 5, 4, 4 (5S, 16S, 23S)
complete rRNAs :: 5, 4, 4 (5S, 16S, 23S)
tRNAs :: 50
ncRNAs :: 4
Pseudo Genes (total) :: 44
CDSs (without protein) :: 44
Pseudo Genes (ambiguous residues) :: 0 of 44
Pseudo Genes (frameshifted) :: 23 of 44
Pseudo Genes (incomplete) :: 22 of 44
Pseudo Genes (internal stop) :: 4 of 44
Pseudo Genes (multiple problems) :: 4 of 44
##Genome-Annotation-Data-END##
COMPLETENESS: full length.
FEATURES Location/Qualifiers
source 1..4226
/organism="Macrococcus caseolyticus JCSC5402"
/mol_type="genomic DNA"
/strain="JCSC5402"
/db_xref="taxon:458233"
/plasmid="pMCCL6"
gene join(4165..4226,1..64)
/locus_tag="MCCL_RS12530"
CDS join(4165..4226,1..64)
/locus_tag="MCCL_RS12530"
/inference="COORDINATES: ab initio
prediction:GeneMarkS-2+"
/note="Derived by automated computational analysis using
gene prediction method: GeneMarkS-2+."
/codon_start=1
/transl_table=11
/product="hypothetical protein"
/protein_id="WP_269446095.1"
/translation="MKTAKKQTANEKRLGTDFSAENVIKLTERQFEKNKAETLCS"
gene 274..663
/locus_tag="MCCL_RS11535"
CDS 274..663
/locus_tag="MCCL_RS11535"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_012657567.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="hypothetical protein"
/protein_id="WP_041636600.1"
/translation="MFEERERIRKEKLELIAKKVGLDREGNFKTPVLFVEHADKPVRY
TYLSSELKRSERGWSSEIAKENVKFDYYVSPHKKLFSAEYRKENGESLYQTCRKGADR
EDVSAEFEKAHTKVKQANMSKGRSKSI"
gene 1132..2037
/locus_tag="MCCL_RS11540"
/old_locus_tag="MCCL_plsF0001"
CDS 1132..2037
/locus_tag="MCCL_RS11540"
/old_locus_tag="MCCL_plsF0001"
/inference="COORDINATES: protein motif:HMM:NF013235.2"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="replication initiation protein"
/protein_id="WP_012657560.1"
/translation="MIDLVKYHNNLNSVVFGKFNANEMNLFFSIISKLKDKGEDTVIF
SWNELKDLSRYKPTATQRFVSDLDKTYKKMLELNYGQTFVKKKRLTYSRFVLFTSFHI
DCDMNDDGDLDASTGIVAIKINPELRHILNDLEQWTQYSLEEFIKLKSTYSKTIFRLL
KQFRTTGYLKLSVEEFREQLDIPNSYRMSHINQKVISVAEKELNAHFKNLKINKIKAK
KKGAPVVAIEFRWSPEKTGTFVDYSKKKQPRELTPKWLKNEGQQNRSTDEMSEEELEI
EREKLRKELAELENAKQTEIDEYIK"
gene 2140..2514
/locus_tag="MCCL_RS11545"
/old_locus_tag="MCCL_plsF0002"
CDS 2140..2514
/locus_tag="MCCL_RS11545"
/old_locus_tag="MCCL_plsF0002"
/inference="COORDINATES: ab initio
prediction:GeneMarkS-2+"
/note="Derived by automated computational analysis using
gene prediction method: GeneMarkS-2+."
/codon_start=1
/transl_table=11
/product="hypothetical protein"
/protein_id="WP_012657561.1"
/translation="MYDKRQELEELEKKRKALLQEIKEKEKEHYKTLLEFYGDDFPRN
DKKRPISLKQFRENYMLIEKKNYENFKTQDDERRLEAYEKIFGVLRKTADNIDYSQGY
PKLPNLSEFTKWVEKFKTKTEI"
gene 3075..3380
/locus_tag="MCCL_RS11550"
/old_locus_tag="MCCL_plsF0003"
CDS 3075..3380
/locus_tag="MCCL_RS11550"
/old_locus_tag="MCCL_plsF0003"
/inference="COORDINATES: ab initio
prediction:GeneMarkS-2+"
/note="Derived by automated computational analysis using
gene prediction method: GeneMarkS-2+."
/codon_start=1
/transl_table=11
/product="hypothetical protein"
/protein_id="WP_012657562.1"
/translation="MSEKKKKKSKIISFRANEDEYEVIAGIAKSANMNISEYLKIRAL
EGNIQQPKVSSEDLRAVVPELTRLTGQIGRIGNNVNQSTKLLSSIGPYGFVSPKNFR"
gene 3447..4196
/locus_tag="MCCL_RS11555"
/old_locus_tag="MCCL_plsF0004"
CDS 3447..4196
/locus_tag="MCCL_RS11555"
/old_locus_tag="MCCL_plsF0004"
/inference="COORDINATES: protein motif:HMM:NF015397.2"
/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_012657563.1"
/translation="MAYTKVAPSKSSGASIVYARDGKDNDKDKCVAMSGLNCDPSNAE
YEFAVVRRAHNKALKEGEDIQARLIIQSFEGEELSPEEVNEMGYELAENINEKLGGGF
QAVVYTHGNTKNLHNHIVFNSVNADTGKKYTMHYEKFEIEKMSDEIVSQRGLNVIEKQ
KKDITTNGERKLRENGQYVWKDDLKDRFNRAFDKTLLNVSKNRTENLEEFKKNLSELG
VNVKERYVKKRDTTYFTYVFTDENGKKTDCK"
CONTIG join(AP009490.1:1..4226)
//
