LOCUS NC_011995 15667 bp DNA circular CON 24-DEC-2022
DEFINITION Macrococcus caseolyticus JCSC5402 plasmid pMCCL1, complete
sequence.
ACCESSION NC_011995
VERSION NC_011995.1
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 15667)
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
AP009485.1.
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..15667
/organism="Macrococcus caseolyticus JCSC5402"
/mol_type="genomic DNA"
/strain="JCSC5402"
/db_xref="taxon:458233"
/plasmid="pMCCL1"
gene complement(join(15183..15667,1..616))
/locus_tag="MCCL_RS11790"
CDS complement(join(15183..15667,1..616))
/locus_tag="MCCL_RS11790"
/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="relaxase/mobilization nuclease domain-containing
protein"
/protein_id="WP_050742487.1"
/translation="MAQTKVASSKSATASIKYGRDGKDKETSKKKCIAMSGINCDPSN
AEYEFGVVRKAFNKAKEEGKDIQTHLIEQSFKGRDIDPYEVNQMGYELAERLNKELGG
GFQAVVYTHGNTNNYHNHIVFNAVNLEDGHKYHCYQEKKIVERINDAIVREHGYPVIE
KNKERGTSVTIKEQKLKDKGEYIWKDDLRDRIDKAFEKTKDSLHFDLERFRAHLTDLG
VNIRERFNQKQQITRFSYDFIDQDGKKRVTREKNLGVDYGAEGIKYGLEQERKSYEQF
KQQQSGFTPSPASRTADIEIPESRDSIQQYARQVLDARIRDAGNERTQREPRTRDEYS
HQRKQSTQDRTSKDHSVKSKQNRQHDRGGLER"
gene complement(598..1041)
/locus_tag="MCCL_RS12345"
/old_locus_tag="MCCL_plsA0001"
CDS complement(598..1041)
/locus_tag="MCCL_RS12345"
/old_locus_tag="MCCL_plsA0001"
/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_041636556.1"
/translation="MTNGHELFFTEWRDEQVSETKKKSKIISFRVNADEYDVIAGTAS
SANLNITSYLKARALGGKIHRPLMKSEDIQSILPPLSKLSGEISRVGNNMNQSTRALR
SLSIETFLGQHEMNEVKKLTEEFNALKQEFEILQSEVHQIWHKLK"
gene complement(1561..1932)
/locus_tag="MCCL_RS10990"
/old_locus_tag="MCCL_plsA0002"
CDS complement(1561..1932)
/locus_tag="MCCL_RS10990"
/old_locus_tag="MCCL_plsA0002"
/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_012655832.1"
/translation="MTNIDYEKELQALEEKKKQLLKEKREKDKKELQTLKEVFGKDFP
RKENGKFISLDEFKKNYVISHKNQSAINPNELNAVQEELNQLKKALNGIANAMDDSRG
YWHINDLKGLTNWLSQFRTKG"
gene 2461..3354
/locus_tag="MCCL_RS10995"
/old_locus_tag="MCCL_plsA0003"
CDS 2461..3354
/locus_tag="MCCL_RS10995"
/old_locus_tag="MCCL_plsA0003"
/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_050742485.1"
/translation="MSVCSLLGHNPEKVEYLDLQLNGDTEKYVDPNMIEYLADRSKGD
LQVLSKQANTQIYSFFNQIIKILKSDENEQKKRIEMNNLFSFFQEPQHLNLGISLEGN
TGKGTTAKELVKTFMREDVVSLILDESGLTIPQKTPLFPYFADDKLSDLTSNIIMNVI
IEFNKKIVVLYPEMSSYLSSVNEEYNYYSNGTWKQMRHKPFIFSEKKVLFIPKDFATY
KQTSSLSLLIRTILVEAIEKDKIKNNREKRKTKKEFEKENIAGNRTENTRKIYDESTE
VSYKYYQKEVINKVKERLTKD"
gene complement(3396..3962)
/locus_tag="MCCL_RS11000"
/old_locus_tag="MCCL_plsA0004"
CDS complement(3396..3962)
/locus_tag="MCCL_RS11000"
/old_locus_tag="MCCL_plsA0004"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_012657302.1"
/GO_function="GO:0003677 - DNA binding [Evidence IEA]"
/GO_process="GO:0006310 - DNA recombination [Evidence
IEA]"
/GO_process="GO:0015074 - DNA integration [Evidence IEA]"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="tyrosine-type recombinase/integrase"
/protein_id="WP_012655834.1"
/translation="MNSVEPIRDVKKIQEMKEALAYYGSERDVFLFNLGINCGLRVSD
MLGLKKKDIKDYTIKLREQKTRKQKQIPLYHLKVDIDRYIQFLENEDYLFKSNKLDSD
GNDKPISRVQAYRILNHSAKSIDLSEIGTHSMRKTFGYHYYKKTKDIALLMDLFNHSS
QSVTLRYIGIRQDMINESISFAMKDLFN"
gene complement(4101..4610)
/locus_tag="MCCL_RS11005"
/old_locus_tag="MCCL_plsA0005"
CDS complement(4101..4610)
/locus_tag="MCCL_RS11005"
/old_locus_tag="MCCL_plsA0005"
/inference="COORDINATES: protein motif:HMM:NF025054.2"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="GNAT family N-acetyltransferase"
/protein_id="WP_012655835.1"
/translation="MTIEKLSNDSIFQFISFLEKSFKDTYQNIYPIEYIEKIINDFYS
PDNIVRDNNKDSEDWQGYYVYLENNKIVGAIAGGQVQDNIYQVFMLYVHPDFQSRGIG
TELLDFITNKQIQYNATTQIVNVSVDNKSAIDYYEYKKFKKIKVVKNWFLYSEYKFKD
YRYSRSLKI"
gene complement(4629..5891)
/locus_tag="MCCL_RS11010"
/old_locus_tag="MCCL_plsA0006"
CDS complement(4629..5891)
/locus_tag="MCCL_RS11010"
/old_locus_tag="MCCL_plsA0006"
/inference="COORDINATES: protein motif:HMM:NF017760.2"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="MFS transporter"
/protein_id="WP_012655836.1"
/translation="MDEINIIKKSYIQMWLRIIATFISEFGSKTFSFGLSFYVYKETQ
STISFGLTLIAIPFATVILAPIIGKIIDTYKHKHIIIISQIFSVIFVTFFLLLNNKIE
NILIPSLVLIIFLSIFDEFVLLTLFASNSSTIHSNHLQKLRGYQQIVSNISMIVAPVL
GAILVASLSFNIFIIIEVLSEVLTLIINVFINFNLISKKDISSENSDLSMKHALSFVK
EQKYLKSLILLSAIVNLSDTIYKIGLPIIVLSIFKLNNTYFGYMESSIIIGSMIGGYI
MAKRKKNTQPLKSLVPLCILTSFLMIIIPLAPFINNIFIGYLLIAFTVLVIHLLESLF
NIPLQVWYVEEVPEYIQGRVFAIMNALMMGSLPLGILSFGALYEVNFYSLIVLNLIAF
LIAITLRISVLLYVKLILKIDLADAKVF"
gene complement(6222..7169)
/locus_tag="MCCL_RS11015"
/old_locus_tag="MCCL_plsA0007"
CDS complement(6222..7169)
/locus_tag="MCCL_RS11015"
/old_locus_tag="MCCL_plsA0007"
/inference="COORDINATES: protein motif:HMM:NF015983.2"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="radical SAM protein"
/protein_id="WP_012655837.1"
/translation="MKQLQFDFPIGMHLELSGKCNLKCKHCYVNSGAPGTVDISDIDL
LDFFESYFNYSFIPQINITGGEAFIRQDLLKDILLLFSKNSPHTHIRLMTNGYFLKED
FFLFLKEIKNKVSFQISLDGANKASHERVRIVDGSWEKALDACLLIKKFNHNLQIATT
ITKSNFYEIEDMFKLSVILNADSIGIGPAYPLGRGIEDKFNLILSDNEIAEAKEQLYV
YKKVYDKYLEVNLTTQLDEHFYNNLSIIKQDWFIIDNMGNVKIDTRLPYIVGNITKHP
IDTLWKKVRHSFENNKVNEDIEKAIEQNTLINNMEKIKL"
gene complement(7150..8364)
/locus_tag="MCCL_RS11020"
/old_locus_tag="MCCL_plsA0008"
CDS complement(7150..8364)
/locus_tag="MCCL_RS11020"
/old_locus_tag="MCCL_plsA0008"
/inference="COORDINATES: protein motif:HMM:NF015983.2"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="radical SAM/SPASM domain-containing protein"
/protein_id="WP_012655838.1"
/translation="MKYFLSPFTTLKNMGNHFILGDLLNKNNIYKFNDPSEIVPENEA
LLNKFFFEYNQQNMNLFLQDSYNSLYILFNNQKNNIGYVETTTVCPYKCQICPKSSNN
QLREQSNLSLDSIDQILKSLKNQNTIAFHLFGDPLYDKDIYKKIQIANSYNIVPSFST
NLISLNKLDLEEIKKCNIGQITISFDAYTEDTLTTIRGKTSQEKIDKGLNNLIKLDKL
ANIYKNIDVIYLQQINLKNNSHEEKYIESLVEKGHIMKFIKKKYINFPLNKNNELGTL
EIINNGETVLFYKLLNKKTPFKCLKPWIKKESAINSDGDYLPCCLSLNNTVDLGNFKS
LSVNNFFNSKELKNLQDEIFFGKITKKNITCAQCYANTSWARLENNNDAFNHLKKYTI
TDWSEYFETITV"
gene complement(8366..9448)
/locus_tag="MCCL_RS11025"
/old_locus_tag="MCCL_plsA0009"
CDS complement(8366..9448)
/locus_tag="MCCL_RS11025"
/old_locus_tag="MCCL_plsA0009"
/inference="COORDINATES: protein motif:HMM:NF013094.2"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="ThiF family adenylyltransferase"
/protein_id="WP_012655839.1"
/translation="MKFIQKEMGCEFFVLDTEIMIVNNNLFKYQIFPKSEYLSSFIKY
LNSDKKIEVKNLNRYIEVPSDILNKIIDKFLKLKLIRLVEVDEIVQGAEFIEQSLDPR
FGTQLLWMNQFTNDAPKLLSNIKNLEVCIIGAGALGSSLALKLSAMGIKNISIWDGDK
VELDNLTRQYLYTDKASQNNEYKVDELKKIIKNFYPESNIRVHRKFINSYKSFYEIEK
NTNLIIQTADFPKGKIDYWCNEYSIKNKIPVIFTHHKSVGPFYIPGKTACLACFENYI
NTQTNGYFKKYKEIVKNKPNQKNGSFITGQLMNEVIILNLFTRFFIKKDYDFSNSIFI
INESDLSIDLLNFDLKHECQCRQGGI"
gene complement(9938..10780)
/locus_tag="MCCL_RS11030"
/old_locus_tag="MCCL_plsA0010"
CDS complement(9938..10780)
/locus_tag="MCCL_RS11030"
/old_locus_tag="MCCL_plsA0010"
/inference="COORDINATES: protein motif:HMM:NF037898.2"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="helix-turn-helix transcriptional regulator"
/protein_id="WP_012655840.1"
/translation="MLNIGEFIKNKRNEMNMTQIQLSNGICTQGQISKIEKGEIDPSS
EILVKIAQKLDFSLDDLFNLTSIEKLNTNKNIMLNIKELINSRNYEQLEHLIKHTDTS
VLNLEDTVYMEWAKLITDYNLYNKDILNDLKKILHNREMNISDKMISIIYNSIGVIHK
QKHDYTHAKYYFKKVRELHSIHPEDFEYILKIYLNLSNILFELEQWEELYETCIESIR
ISYNSNNMVVLPELIYSKNYSLNKISNSFQCNIDELNFALFLAEKQNKIIVKEMIEKY
LTNI"
gene complement(10800..11000)
/locus_tag="MCCL_RS11035"
CDS complement(10800..11000)
/locus_tag="MCCL_RS11035"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_002448025.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="hypothetical protein"
/protein_id="WP_041636559.1"
/translation="MSGFLDNIDTSEVKYTPNYRVTKESATIRVRKDIKKRLEHMKLD
KDIKMIDIASEVLEKYLRENGY"
gene complement(11007..11798)
/locus_tag="MCCL_RS11040"
/old_locus_tag="MCCL_plsA0011"
CDS complement(11007..11798)
/locus_tag="MCCL_RS11040"
/old_locus_tag="MCCL_plsA0011"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_020366803.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="ParA family protein"
/protein_id="WP_012655841.1"
/translation="MTVITIGNFKGGVGKTTVSTMLCYIASEHYDKKVLLVDFDPQGN
ASAIMKRTFPNHSENKMSLIDALKTNDINNCKIHLSENLDLLPAEPSLANLSDEIAKN
NIQTKRYILKRVLDTIKDQYDLVFIDVPPTINSDFTNNAVYASDFIVMVFQTQQSAYE
SSLAFVNFLRDRKKESDLSFDLIGAIPVLIKKNGLIDAQIIEKSKKTFGAALFENQIY
QRERIKKFGAEGIKNEDIHDKMVMKMFNDIYLELFERLSIIYDKG"
gene 12284..13783
/locus_tag="MCCL_RS11045"
/old_locus_tag="MCCL_plsA0012"
CDS 12284..13783
/locus_tag="MCCL_RS11045"
/old_locus_tag="MCCL_plsA0012"
/inference="COORDINATES: protein motif:HMM:NF020291.2"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="primase C-terminal domain-containing protein"
/protein_id="WP_012655842.1"
/translation="MQIYQEDVQDILTTLMNNGLRETRYKKSKLNIVEPVSKYRTGKI
IVTRSKEELKGAKGVIVGSIEALLDNHPNLTHITPNVYRSAKNLSNGGVKGHSERNLK
QINAFIIDIDGVDKSVITLADIVLRGHEVGLRPTLVLHTPKGYHVYFMLKEPIYIKKT
SGHNNALDKAKRISLNLRKYYAEVIPGIDITCNHFGFFRCPNKDNIIDYSPESRYSMS
DFINFSIKYESLNMNESQKHFNNNIIPFKQLKNIHEPWFHLLYNCKHIKGHGEQIGRD
NAIFTMALHMYASKLSKAEAIEMLAHFNKNLKHPLEHSIVVQKVNSAYSGKYKGASKL
YIYKLLYAWCEITEKIKNRLFFRNHAKVRKDRLRSHYSEWKEDLYQYIKSKETNGYLE
ITTKELCEALGIPKSTLKEVLKKYDTFIWSATKGKYAKLKITTKDIIINNLLKKIKTN
NMNIQRLRVELYKFLRGINLSSIEKTNILRNIQLDSNEKLETASRENTS"
gene complement(14377..14997)
/locus_tag="MCCL_RS11050"
/old_locus_tag="MCCL_plsA0013"
CDS complement(14377..14997)
/locus_tag="MCCL_RS11050"
/old_locus_tag="MCCL_plsA0013"
/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_012655843.1"
/translation="MFTFLYYVMPVCIIALCLFGMFLWLSSQIDHLRSLRFTVPVSLI
VFIIGITMSTWTPLSPLPFYQQHLHVQKVNEQYKVAESYLDNLMNKGFLDFNTTVKKH
VTHRHFSVAQQKINRIDDREKRKSLMNKHSEYLAIYEQRIGDNLIRKIQLEHLSVSEY
NQLTAQEYNNVRYQIRQQIQNPQTEKDFLEHVQKLQKDHDSLYNYR"
gene complement(14999..15193)
/locus_tag="MCCL_RS12125"
CDS complement(14999..15193)
/locus_tag="MCCL_RS12125"
/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_050742486.1"
/translation="MNAKKLKQTVLTDIKRDLKSEMDSYQQELNKGYLKSNIFLNYVP
VIISLIFVIFIIYYLMIGMH"
CONTIG join(AP009485.1:1..15667)
//
