Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 8-Mar-2022 from the annotated genome of Kocuria salsicia G1, as obtained from RefSeq (see the RefSeq entry for the authors of the original genome sequence). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [Caspi20]. It has not undergone any manual curation or review, and may contain errors. Development of this PGDB was supported by grant GM080746 from the National Institutes of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_CZJU0100014375750075,996RefSeq:NZ_CZJU01000143
NZ_CZJU0100009854500463,684RefSeq:NZ_CZJU01000098
NZ_CZJU0100012856540263,135RefSeq:NZ_CZJU01000128
NZ_CZJU0100009950454161,162RefSeq:NZ_CZJU01000099
NZ_CZJU0100010145440157,427RefSeq:NZ_CZJU01000101
NZ_CZJU0100011251473155,792RefSeq:NZ_CZJU01000112
NZ_CZJU0100011949470254,618RefSeq:NZ_CZJU01000119
NZ_CZJU0100011350491053,019RefSeq:NZ_CZJU01000113
NZ_CZJU0100013448471050,827RefSeq:NZ_CZJU01000134
NZ_CZJU0100012937361049,847RefSeq:NZ_CZJU01000129
NZ_CZJU0100014440381142,875RefSeq:NZ_CZJU01000144
NZ_CZJU0100006540351441,475RefSeq:NZ_CZJU01000065
NZ_CZJU0100017534322041,310RefSeq:NZ_CZJU01000175
NZ_CZJU0100013635332040,944RefSeq:NZ_CZJU01000136
NZ_CZJU0100013737360140,610RefSeq:NZ_CZJU01000137
NZ_CZJU0100012132291240,448RefSeq:NZ_CZJU01000121
NZ_CZJU0100010733320139,776RefSeq:NZ_CZJU01000107
NZ_CZJU0100006822211039,284RefSeq:NZ_CZJU01000068
NZ_CZJU0100018838361138,970RefSeq:NZ_CZJU01000188
NZ_CZJU0100012533330038,229RefSeq:NZ_CZJU01000125
NZ_CZJU0100012235350037,499RefSeq:NZ_CZJU01000122
NZ_CZJU0100013935340136,373RefSeq:NZ_CZJU01000139
NZ_CZJU0100009233321035,437RefSeq:NZ_CZJU01000092
NZ_CZJU0100011731282134,830RefSeq:NZ_CZJU01000117
NZ_CZJU0100008632280434,516RefSeq:NZ_CZJU01000086
NZ_CZJU0100010628271034,268RefSeq:NZ_CZJU01000106
NZ_CZJU0100015635304133,902RefSeq:NZ_CZJU01000156
NZ_CZJU0100008529280133,709RefSeq:NZ_CZJU01000085
NZ_CZJU0100012029270233,529RefSeq:NZ_CZJU01000120
NZ_CZJU0100009030261333,264RefSeq:NZ_CZJU01000090
NZ_CZJU0100017228280032,813RefSeq:NZ_CZJU01000172
NZ_CZJU0100008328242232,470RefSeq:NZ_CZJU01000083
NZ_CZJU0100010428260231,491RefSeq:NZ_CZJU01000104
NZ_CZJU0100007829281031,061RefSeq:NZ_CZJU01000078
NZ_CZJU0100012329290030,026RefSeq:NZ_CZJU01000123
NZ_CZJU0100010323183229,479RefSeq:NZ_CZJU01000103
NZ_CZJU0100013322210129,215RefSeq:NZ_CZJU01000133
NZ_CZJU0100007026250128,317RefSeq:NZ_CZJU01000070
NZ_CZJU0100007617170027,796RefSeq:NZ_CZJU01000076
NZ_CZJU0100008025241025,864RefSeq:NZ_CZJU01000080
NZ_CZJU0100007426251025,006RefSeq:NZ_CZJU01000074
NZ_CZJU0100009621180324,732RefSeq:NZ_CZJU01000096
NZ_CZJU0100007224240024,048RefSeq:NZ_CZJU01000072
NZ_CZJU0100007724210323,817RefSeq:NZ_CZJU01000077
NZ_CZJU0100006622220023,804RefSeq:NZ_CZJU01000066
NZ_CZJU0100007519180123,259RefSeq:NZ_CZJU01000075
NZ_CZJU0100009119190022,672RefSeq:NZ_CZJU01000091
NZ_CZJU0100007319190021,179RefSeq:NZ_CZJU01000073
NZ_CZJU0100012416160021,099RefSeq:NZ_CZJU01000124
NZ_CZJU0100013016140221,033RefSeq:NZ_CZJU01000130
NZ_CZJU0100006318180021,005RefSeq:NZ_CZJU01000063
NZ_CZJU0100013523230020,147RefSeq:NZ_CZJU01000135
NZ_CZJU0100014119180119,623RefSeq:NZ_CZJU01000141
NZ_CZJU0100014217160119,421RefSeq:NZ_CZJU01000142
NZ_CZJU0100014515141019,305RefSeq:NZ_CZJU01000145
NZ_CZJU0100014613121019,098RefSeq:NZ_CZJU01000146
NZ_CZJU0100008118160218,740RefSeq:NZ_CZJU01000081
NZ_CZJU0100015019172018,512RefSeq:NZ_CZJU01000150
NZ_CZJU0100015217150217,984RefSeq:NZ_CZJU01000152
NZ_CZJU0100015317170017,972RefSeq:NZ_CZJU01000153
NZ_CZJU0100015517170017,485RefSeq:NZ_CZJU01000155
NZ_CZJU0100015715150017,307RefSeq:NZ_CZJU01000157
NZ_CZJU0100019617170017,039RefSeq:NZ_CZJU01000196
NZ_CZJU0100015914140016,938RefSeq:NZ_CZJU01000159
NZ_CZJU0100016114140016,556RefSeq:NZ_CZJU01000161
NZ_CZJU0100014013130016,416RefSeq:NZ_CZJU01000140
NZ_CZJU0100006216151016,395RefSeq:NZ_CZJU01000062
NZ_CZJU0100011415150016,145RefSeq:NZ_CZJU01000114
NZ_CZJU0100008913121016,142RefSeq:NZ_CZJU01000089
NZ_CZJU0100016318180016,142RefSeq:NZ_CZJU01000163
NZ_CZJU0100008211110015,051RefSeq:NZ_CZJU01000082
NZ_CZJU0100016812110114,979RefSeq:NZ_CZJU01000168
NZ_CZJU0100012613130014,840RefSeq:NZ_CZJU01000126
NZ_CZJU0100016913130014,715RefSeq:NZ_CZJU01000169
NZ_CZJU0100010814140014,557RefSeq:NZ_CZJU01000108
NZ_CZJU010001271170414,456RefSeq:NZ_CZJU01000127
NZ_CZJU0100017813130014,173RefSeq:NZ_CZJU01000178
NZ_CZJU0100010211100114,109RefSeq:NZ_CZJU01000102
NZ_CZJU0100010516150113,661RefSeq:NZ_CZJU01000105
NZ_CZJU0100018412120012,904RefSeq:NZ_CZJU01000184
NZ_CZJU0100019212110110,702RefSeq:NZ_CZJU01000192
NZ_CZJU0100019711101010,396RefSeq:NZ_CZJU01000197
117 Undisplayed Contigs/Replicons4394261341610,733
Total:2,5942,432561062,999,584
Ortholog data available?Yes
Database Contents
Genes2,594
Pathways220
Enzymatic Reactions1,099
Transport Reactions42
Polypeptides2,533
Protein Complexes1
Enzymes642
Transporters280
Compounds833
Transcription Units1,928
tRNAs48
Protein Features3,090
GO Terms208
Database Version29.0
Sequence SourceGCF_001408335.1
Synonyms Kocuria sp. 104
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Micrococcales
Micrococcaceae
Kocuria
Kocuria salsicia
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMEA3489743
NCBI BioProjectPRJNA224116
NCBI-Taxonomy664639
EnvironmentMeat Chopper / Grinder in a Danish Slaughterhouse
Annotation ProviderNCBI RefSeq
Annotation Date2021-12-19
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp16: Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R (2016). "Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform 17(5);877-90. PMID: 26454094

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